Treatment is often started without confirmation of infection because of the serious complications that may result from delayed treatment. Treatment depends on the infectious agent and generally involves the use of antibiotic therapy. If there is no improvement within two to three days, the patient is typically advised to seek further medical attention. Hospitalization sometimes becomes necessary if there are other complications. Treating sexual partners for possible STIs can help in treatment and prevention.

For women with PID of mild to moderate severity, parenteral and oral therapies appear to be effective. It does not matter to their short- or long-term outcome whether antibiotics are administered to them as inpatients or outpatients. Typical regimens include cefoxitin or cefotetan plus doxycycline, and clindamycin plus gentamicin. An alternative parenteral regimen is ampicillin/sulbactam plus doxycycline. Erythromycin-based medications can also be used. Another alternative is to use a parenteral regimen with ceftriaxone or cefoxitin plus doxycycline. Clinical experience guides decisions regarding transition from parenteral to oral therapy, which usually can be initiated within 24–48 hours of clinical improvement.

If tubal factor infertility is suspected to be the cause of the infertility treatment begins with or without confirmation of infection because of complications that may result from delayed treatment. Appropriate treatment depends on the infectious agent and utilizes antibiotic therapy. Treating the sexual partner for possible STIs helps in treatment and prevents reinfection.

Antibiotic administration affects the short or long-term major outcome of women with mild or moderate disease.

For women with infections of mild to moderate severity, parenteral and oral therapies are prescribed . Typical antibiotics used are cefoxitin or cefotetan plus doxycycline, and clindamycin plus gentamicin. An alternative parenteral regimen is ampicillin/sulbactam plus doxycycline. Once infection has been eliminated, surgery may be successful in opening the lumen of the fallopian tubes to allow a successful pregnancy and birth.

In both the acute and chronic forms, antibiotics are used if an infection is suspected. The treatment of choice is often azithromycin and cefixime to cover both gonorrhoeae and chlamydia. Fluoroquinolones are no longer recommended due to widespread resistance of gonorrhoeae to this class. Doxycycline may be used as an alternative to azithromycin. In chronic epididymitis, a four- to six-week course of antibiotics may be prescribed to ensure the complete eradication of any possible bacterial cause, especially the various chlamydiae.

For cases caused by enteric organisms (such as "E. coli"), ofloxacin or levofloxacin are recommended.

In children, fluoroquinolones and doxycycline are best avoided. Since bacteria that cause urinary tract infections are often the cause of epididymitis in children, co-trimoxazole or suited penicillins (for example, cephalexin) can be used.

Household remedies such as elevation of the scrotum and cold compresses applied regularly to the scrotum may relieve the pain in acute cases. Painkillers or anti-inflammatory drugs are often used for treatment of both chronic and acute forms. Hospitalisation is indicated for severe cases, and check-ups can ensure the infection has cleared up. Surgical removal of the epididymis is rarely necessary, causes sterility, and only gives relief from pain in approximately 50% of cases. However, in acute suppurating epididymitis (acute epididymitis with a discharge of pus), a epididymotomy may be recommended; in refractory cases, a full epididymectomy may be required. In cases with unrelenting testicular pain, removal of the entire testicle—orchiectomy—may also be warranted.

It is generally believed that most cases of chronic epididymitis will eventually "burn out" of patient's system if left untreated, though this might take years or even decades. However, some prostate-related medications have proven effective in treating chronic epididymitis, including doxazosin.

Even when the PID infection is cured, effects of the infection may be permanent. This makes early identification essential. Treatment resulting in cure is very important in the prevention of damage to the reproductive system. Formation of scar tissue due to one or episodes of PID can lead to tubal blockage, increasing the risk of the inability to get pregnant and long-term pelvic/abdominal pain. Certain occurrences such as a post pelvic operation, the period of time immediately after childbirth (postpartum), miscarriage or abortion increase the risk of acquiring another infection leading to PID.

Over time, the relapse rate is high, exceeding 50%. However, recent research indicates that combination therapies offer a better prognosis than antibiotics alone.

A 2007 study showed that repeated combination pharmacological therapy with antibacterial agents (ciprofloxacin/azithromycin), alpha-blockers (alfuzosin) and Serenoa repens extracts may eradicate infection in 83.9% of patients with clinical remission extending throughout a follow-up period of 30 months for 94% of these patients.

A 2014 study of 210 patients randomized into two treatment groups found that recurrence occurred within 2 months in 27.6% of the group using antibiotics alone (prulifloxacin 600 mg), but in only 7.8% of the group taking prulifloxacin in combination with Serenoa repens extract, Lactobacillus Sporogens and Arbutin.

Antibiotic therapy has to overcome the blood/prostate barrier that prevents many antibiotics from reaching levels that are higher than minimum inhibitory concentration. A blood-prostate barrier restricts cell and molecular movement across the rat ventral prostate epithelium. Treatment requires prolonged courses (4–8 weeks) of antibiotics that penetrate the prostate well. The fluoroquinolones, tetracyclines and macrolides have the best penetration. There have been contradictory findings regarding the penetrability of nitrofurantoin , quinolones (ciprofloxacin, levofloxacin), sulfas (Bactrim, Septra), doxycycline and macrolides (erythromycin, clarithromycin). This is particularly true for gram-positive infections.

In a review of multiple studies, Levofloxacin (Levaquin) was found to reach prostatic fluid concentrations 5.5 times higher than Ciprofloxacin, indicating a greater ability to penetrate the prostate.

Persistent infections may be helped in 80% of patients by the use of alpha blockers (tamsulosin (Flomax), alfuzosin), or long term low dose antibiotic therapy. Recurrent infections may be caused by inefficient urination (benign prostatic hypertrophy, neurogenic bladder), prostatic stones or a structural abnormality that acts as a reservoir for infection.

In theory, the ability of some strains of bacteria to form biofilms might be one factor amongst others to facilitate development of chronic bacterial prostatitis.

Escherichia coli extract and cranberry have a potentially preventive effect on the development of chronic bacterial prostatitis, while combining antibiotics with saw palmetto, lactobacillus sporogens and arbutin may lead to better treatment outcomes.

Bacteriophages hold promise as another potential treatment for chronic bacterial prostatatis.

The addition of prostate massage to courses of antibiotics was previously proposed as being beneficial and prostate massage may mechanically break up the biofilm and enhance the drainage of the prostate gland. However, in more recent trials, this was not shown to improve outcome compared to antibiotics alone.

A number of medications can be used to treat this disorder. Alpha blockers and/or antibiotics appear to be the most effective with NSAIDs such as ibuprofen providing lesser benefit.

- Treatment with antibiotics is controversial. Some have found benefits in symptoms while others have questioned the utility of a trial of antibiotics. Antibiotics are known to have anti-inflammatory properties and this has been suggested as an explanation for their partial efficacy in treating CPPS. Antibiotics such as fluoroquinolones, tetracyclines, and macrolides have direct anti-inflammatory properties in the absence of infection, blocking inflammatory chemical signals (cytokines) such as interleukin-1 (IL-1), interleukin-8 and tumor necrosis factor (TNF), which coincidentally are the same cytokines found to be elevated in the semen and EPS of men with chronic prostatitis.

- The effectiveness of alpha blockers (tamsulosin, alfuzosin) is questionable in men with CPPS. A 2006 meta-analysis found that they are moderately beneficial when the duration of therapy was at least 3 months.

- An estrogen reabsorption inhibitor such as mepartricin improves voiding, reduces urological pain and improves quality of life in patients with chronic non-bacterial prostatitis.

- Therapies that have not been properly evaluated in clinical trials although there is supportive anecdotal evidence include gabapentin, benzodiazepines, and amitriptyline.

Transurethral needle ablation of the prostate (TUNA) has been shown to be ineffective in trials.

Treatment involves antibiotics and may involve drainage of the buboes or abscesses by needle aspiration or incision. Further supportive measure may need to be taken: dilatation of the rectal stricture, repair of rectovaginal fistulae, or colostomy for rectal obstruction.

Common antibiotic treatments include: tetracycline (doxycycline) (all tetracyclines, including doxycycline, are contraindicated during pregnancy and in children due to effects on bone development and tooth discoloration), and erythromycin. Azithromycin is also a drug of choice in LGV.

As with all STIs, sex partners of patients who have LGV should be examined and tested for urethral or cervical chlamydial infection. After a positive culture for chlamydia, clinical suspicion should be confirmed with testing to distinguish serotype. Antibiotic treatment should be started if they had sexual contact with the patient during the 30 days preceding onset of symptoms in the patient. Patients with a sexually transmitted disease should be tested for other STDs due to high rates of comorbid infections. Antibiotics are not without risks and prophylaxtic broad antibiotic coverage is not recommended.

If symptomatic, testing is recommended. The risk of contracting Micoplasma infection can be reduced by the following:

- Using barrier methods such as condoms

- Seeking medical attention if you are experiencing symptoms suggesting a sexually transmitted infection.

- Seeking medical attention after learning that a current or former sex partner has, or might have had a sexually transmitted infection.

- Getting a STI history from your current partner and insisting they be tested and treated before intercourse.

- Avoiding vaginal activity, particularly intercourse, after the end of a pregnancy (delivery, miscarriage, or abortion) or certain gynecological procedures, to ensure that the cervix closes.

- Abstinence

Mycoplasmas have a triple-layered membrane and lack a cell wall. Commonly used antibiotics are generally ineffective because their efficacy is due to their ability to inhibit cell wall synthesis. Micoplasmas are not affected by penicillins and other antibiotics that act on the cell wall. The growth of micoplasmas in their host is inhibited by other broad-spectrum antibiotics. These broad-spectrum antibiotics inhibit the multiplication of the mycoplasma but does not kill them. Tetracyclines, macrolides, erythromycin, macrolides, ketolides, quinolones are used to treat mycoplasma infections. In addition to the penicillins, mycoplasmas are resistant to rifampicin. Mycoplasmas may be difficult to eradicate from human or animal hosts or from cell cultures by antibiotic treatment because of resistance to the antibiotic, or because it does not kill the mycoplasma cell. Mycoplasma cells are able to invade the cells of their hosts.

Pyometra describes an accumulation of pus in the uterine cavity. In order for pyometra to develop, there must be both an infection "and" blockage of cervix. Signs and symptoms include lower abdominal pain (suprapubic), rigors, fever, and the discharge of pus on introduction of a sound into the uterus.

Pyometra is treated with antibiotics, according to culture and sensitivity.

It's been theorized that retrograde menstrual flow and the cervix opening during menstruation allows the infection to reach the Fallopian tubes.

Other risk factors include surgical procedures that break the cervical barrier, such as:

- endometrial biopsy

- curettage

- hysteroscopy

Another risk is factors that alter the microenvironment in the vagina and cervix, allowing infecting organisms to proliferate and eventually ascend to the Fallopian tube:

- antibiotic treatment

- ovulation

- menstruation

- sexually transmitted disease (STD)

Finally, sexual intercourse may facilitate the spread of disease from the vagina to the Fallopian tube. Coital risk factors are:

- Uterine contractions

- Sperm, carrying organisms upward

The bacteria most associated with salpingitis are:

- N. gonorrhoeae

- Chlamydia trachomatis

- Mycoplasma

- Staphylococcus

- Streptococcus

However, salpingitis is usually polymicrobial, involving many kinds of organisms. Other examples of organisms involved are:

- Ureaplasma urealyticum

- Anaerobic and aerobic bacteria

Oophoritis is an inflammation of the ovaries.

It is often seen in combination with salpingitis (inflammation of the fallopian tubes). It may develop in response to infection.

Recovery from an anaerobic infection depends on adequate and rapid management. The main principles of managing anaerobic infections are neutralizing the toxins produced by anaerobic bacteria, preventing the local proliferation of these organisms by altering the environment and preventing their dissemination and spread to healthy tissues.

Toxin can be neutralized by specific antitoxins, mainly in infections caused by Clostridia (tetanus and botulism). Controlling the environment can be attained by draining the pus, surgical debriding of necrotic tissue, improving blood circulation, alleviating any obstruction and by improving tissue oxygenation. Therapy with hyperbaric oxygen (HBO) may also be useful. The main goal of antimicrobials is in restricting the local and systemic spread of the microorganisms.

The available parenteral antimicrobials for most infections are metronidazole, clindamycin, chloramphenicol, cefoxitin, a penicillin (i.e. ticarcillin, ampicillin, piperacillin) and a beta-lactamase inhibitor (i.e. clavulanic acid, sulbactam, tazobactam), and a carbapenem (imipenem, meropenem, doripenem, ertapenem). An antimicrobial effective against Gram-negative enteric bacilli (i.e. aminoglycoside) or an anti-pseudomonal cephalosporin (i.e. cefepime ) are generally added to metronidazole, and occasionally cefoxitin when treating intra-abdominal infections to provide coverage for these organisms. Clindamycin should not be used as a single agent as empiric therapy for abdominal infections. Penicillin can be added to metronidazole in treating of intracranial, pulmonary and dental infections to provide coverage against microaerophilic streptococci, and Actinomyces.

Oral agents adequate for polymicrobial oral infections include the combinations of amoxicillin plus clavulanate, clindamycin and metronidazole plus a macrolide. Penicillin can be added to metronidazole in the treating dental and intracranial infections to cover "Actinomyces" spp., microaerophilic streptococci, and "Arachnia" spp. A macrolide can be added to metronidazole in treating upper respiratory infections to cover "S. aureus" and aerobic streptococci. Penicillin can be added to clindamycin to supplement its coverage against "Peptostreptococcus" spp. and other Gram-positive anaerobic organisms.

Doxycycline is added to most regimens in the treatment of pelvic infections to cover chlamydia and mycoplasma. Penicillin is effective for bacteremia caused by non-beta lactamase producing bacteria. However, other agents should be used for the therapy of bacteremia caused by beta-lactamase producing bacteria.

Because the length of therapy for anaerobic infections is generally longer than for infections due to aerobic and facultative anaerobic bacteria, oral therapy is often substituted for parenteral treatment. The agents available for oral therapy are limited and include amoxacillin plus clavulanate, clindamycin, chloramphenicol and metronidazole.

In 2010 the American Surgical Society and American Society of Infectious Diseases have updated their guidelines for the treatment of abdominal infections.

The recommendations suggest the following:

For mild-to-moderate community-acquired infections in adults, the agents recommended for empiric regimens are: ticarcillin- clavulanate, cefoxitin, ertapenem, moxifloxacin, or tigecycline as single-agent therapy or combinations of metronidazole with cefazolin, cefuroxime, ceftriaxone, cefotaxime, levofloxacin, or ciprofloxacin. Agents no longer recommended are: cefotetan and clindamycin ( Bacteroides fragilis group resistance) and ampicillin-sulbactam (E. coli resistance) and ainoglycosides (toxicity).

For high risk community-acquired infections in adults, the agents recommended for empiric regimens are: meropenem, imipenem-cilastatin, doripenem, piperacillin-tazobactam, ciprofloxacin or levofloxacin in combination with metronidazole, or ceftazidime or cefepime in combination with metronidazole. Quinolones should not be used unless hospital surveys indicate >90% susceptibility of "E. coli" to quinolones.

Aztreonam plus metronidazole is an alternative, but addition of an agent effective against gram-positive cocci is recommended. The routine use of an aminoglycoside or another second agent effective against gram-negative facultative and aerobic bacilli is not recommended in the absence of evidence that the infection is caused by resistant organisms that require such therapy.

Empiric use of agents effective against enterococci is recommended and agents effective against methicillin-resistant "S. aureus" (MRSA) or yeast is not recommended in the absence of evidence of infection due to such organisms.

Empiric antibiotic therapy for health care-associated intra-abdominal should be driven by local microbiologic results. Empiric coverage of likely pathogens may require multidrug regimens that include agents with expanded spectra of activity against gram-negative aerobic and facultative bacilli. These include meropenem, imipenem-cilastatin, doripenem, piperacillin-tazobactam, or ceftazidime or cefepime in combination with metronidazole. Aminoglycosides or colistin may be required.

Antimicrobial regimens for children include an aminoglycoside-based regimen, a carbapenem (imipenem, meropenem, or ertapenem), a beta-lactam/beta-lactamase-inhibitor combination (piperacillin-tazobactam or ticarcillin-clavulanate), or an advanced-generation cephalosporin (cefotaxime, ceftriaxone, ceftazidime, or cefepime) with metronidazole.

Clinical judgment, personal experience, safety and patient compliance should direct the physician in the choice of the appropriate antimicrobial agents. The length of therapy generally ranges between 2 and 4 weeks, but should be individualized depending on the response. In some instances treatment may be required for as long as 6–8 weeks, but can often be shortened with proper surgical drainage.

Acute Endometritis is characterized by infection. The organisms most often isolated are believed to be because of compromised abortions, delivery, medical instrumentation, and retention of placental fragments. There is not enough evidence for the use of prophylactic antibiotics to prevent endometritis after manual removal of placental in vaginal birth. Histologically, neutrophilic infiltration of the endometrial tissue is present during acute endometritis. The clinical presentation is typically high fever and purulent vaginal discharge. Menstruation after acute endometritis is excessive and in uncomplicated cases can resolve after 2 weeks of clindamycin and gentamicin IV antibiotic treatment.

In certain populations, it has been associated with "Mycoplasma genitalium" and pelvic inflammatory disease.

Though urinary tract infections in men are rare, bacterial infection is the most common cause of acute epididymitis. The bacteria in the urethra back-track through the urinary and reproductive structures to the epididymis. In rare circumstances, the infection reaches the epididymis via the bloodstream.

In sexually active men, "Chlamydia trachomatis" is responsible for two-thirds of acute cases, followed by "Neisseria gonorrhoeae" and "E. coli" (or other bacteria that cause urinary tract infection). Particularly among men over age 35 in whom the cause is "E. coli", epididymitis is commonly due to urinary tract obstruction. Less common microbes include "Ureaplasma", Mycobacterium, and "cytomegalovirus", or "Cryptococcus" in patients with HIV infection. "E. coli" is more common in boys before puberty, the elderly, and men who have sex with men. In the majority of cases in which bacteria are the cause, only one side of the scrotum or the other is the locus of pain.

Non-infectious causes are also possible. Reflux of sterile urine (urine without bacteria) through the ejaculatory ducts may cause inflammation with obstruction. In children, it may be a response following an infection with enterovirus, adenovirus or "Mycoplasma pneumoniae". Rare non-infectious causes of chronic epididymitis include sarcoidosis (more prevalent in black men) and Behçet's disease.

Any form of epididymitis can be caused by genito-urinary surgery, including prostatectomy and urinary catheterization. Congestive epididymitis is a long-term complication of vasectomy. Chemical epididymitis may also result from drugs such as amiodarone.

Most sinusitis cases are caused by viruses and resolve without antibiotics. However, if symptoms do not resolve within 10 days, amoxicillin is a reasonable antibiotic to use first for treatment with amoxicillin/clavulanate being indicated when the person's symptoms do not improve after 7 days on amoxicillin alone. A 2012 Cochrane review, however, found only a small benefit between 7 and 14 days, and could not recommend the practice when compared to potential complications and risk of developing resistance. Antibiotics are specifically not recommended in those with mild / moderate disease during the first week of infection due to risk of adverse effects, antibiotic resistance, and cost.

Fluoroquinolones, and a newer macrolide antibiotic such as clarithromycin or a tetracycline like doxycycline, are used in those who have severe allergies to penicillins. Because of increasing resistance to amoxicillin the 2012 guideline of the Infectious Diseases Society of America recommends amoxicillin-clavulanate as the initial treatment of choice for bacterial sinusitis. The guidelines also recommend against other commonly used antibiotics, including azithromycin, clarithromycin, and trimethoprim/sulfamethoxazole, because of growing antibiotic resistance. The FDA recommends against the use of fluoroquinolones when other options are available due to higher risks of serious side effects.

A short-course (3–7 days) of antibiotics seems to be just as effective as the typical longer-course (10–14 days) of antibiotics for those with clinically diagnosed acute bacterial sinusitis without any other severe disease or complicating factors. The IDSA guideline suggest five to seven days of antibiotics is long enough to treat a bacterial infection without encouraging resistance. The guidelines still recommend children receive antibiotic treatment for ten days to two weeks.

For unconfirmed acute sinusitis, intranasal corticosteroids have not been found to be better than a placebo either alone or in combination with antibiotics. For cases confirmed by radiology or nasal endoscopy, treatment with corticosteroids alone or in combination with antibiotics is supported. The benefit, however, is small.

There is only limited evidence to support short treatment with oral corticosteroids for chronic rhinosinusitis with nasal polyps.

Tubal factor infertility (TFI) is female infertility caused by diseases, obstructions, damage, scarring, congenital malformations or other factors which impede the descent of a fertilized or unfertilized ovum into the uterus through the Fallopian tubes and prevents a normal pregnancy and full term birth. Tubal factors cause 25-30% of infertility cases. Tubal factor is one complication of Chlamydia trachomatis infection in women.

Sexually transmitted Chlamydia and genital mycoplasma infections are preventable causes of infertility and negative pregnancy outcomes. When the infections progress and ascend, they can result in TFI. Infertility can have multiple possible causes and may not be recognized for years after a gonorrhea, Chlamydia or Mycoplasma infection has caused tubal damage, as the affected woman may not have attempted to become pregnant until years later.

Physicians often prescribe the antibiotic trimethoprim-sulfamethoxazole to prevent bacterial infections. This drug also has the benefit of sparing the normal bacteria of the digestive tract. Fungal infection is commonly prevented with itraconazole, although a newer drug of the same type called voriconazole may be more effective. The use of this drug for this purpose is still under scientific investigation.

Long term randomized clinical trials need to be conducted to determine if regular routine scaling and polishing is clinically effective for reducing the risk of chronic periodontitis in healthy adults.

Lasers are increasingly being used in treatments for chronic periodontitis. However, there is some controversy over their use:

"No consistent evidence supports the efficacy of laser treatment as an adjunct to non-surgical periodontal treatment in adults with chronic periodontitis."

Laryngopharyngeal reflux treatment primarily involves behavioural management and medication. Behavioural management involves aspects such as

- Wearing loose clothing

- Eating smaller, more frequent meals

- Avoiding certain foods (e.g. caffeine, alcohol, spicy foods)

Anti-reflux medications may be prescribed for patients with signs of chronic laryngitis and hoarse voice. If anti-reflux treatment does not result in a decrease of symptoms, other possible causes should be examined. Over-the-counter medications for neutralizing acids (antacids) and acid suppressants (H-2 blockers) may be used. Antacids are often short-acting and may not be sufficient for treatment. Proton pump inhibitors are an effective type of medication. These should only be prescribed for a set period of time, after which the symptoms should be reviewed. Proton pump inhibitors do not work for everyone. A physical reflux barrier (e.g. Gaviscon Liquid) may be more appropriate for some. Antisecretory medications can have several side-effects.

When appropriate, anti-reflux surgery may benefit some individuals.