Treatment for TOA differs from PID in that some clinicians recommend patients with tubo-ovarian abscesses have at least 24 hours of inpatient parenteral treatment with antibiotics, and that they may require surgery. If surgery becomes necessary, pre-operative administration of broad-spectrum antibiotics is started and removal of the abscess, the affected ovary and fallopian tube is done. After discharge from the hospital, oral antibiotics are continued for the length of time prescribed by the physician.

Treatment is different if the TOA is discovered before it ruptures and can be treated with IV antibiotics. During this treatment, IV antibiotics are usually replaced with oral antibiotics on an outpatient basis. Patients are usually seen three days after hospital discharge and then again one to two weeks later to confirm that the infection has cleared. Ampicillin/sulbactam plus doxycycline is effective against C. trachomatis, N. gonorrhoeae, and anaerobes in women with tubo-ovarian abscess. Parenteral Regimens described by the Centers for Disease Control and prevention are Ampicillin/Sulbactam 3 g IV every 6 hours and Doxycycline 200 mg orally or IV every 24 hours, though other regiemes that are used for pelvic inflammatory disease have been effective.

Antibiotics are the first line of treatment in acute prostatitis. Antibiotics usually resolve acute prostatitis infections in a very short time, however a minimum of two to four weeks of therapy is recommended to eradicate the offending organism completely. Appropriate antibiotics should be used, based on the microbe causing the infection. Some antibiotics have very poor penetration of the prostatic capsule, others, such as ciprofloxacin, trimethoprim/sulfamethoxazole, and tetracyclines such as doxycycline penetrate prostatic tissue well. In acute prostatitis, penetration of the prostate is not as important as for category II because the intense inflammation disrupts the prostate-blood barrier. It is more important to choose a bactericidal antibiotic (kills bacteria, e.g., a fluoroquinolone antibiotic) rather than a bacteriostatic antibiotic (slows bacterial growth, e.g. tetracycline) for acute potentially life-threatening infections.

Severely ill patients may need hospitalization, while nontoxic patients can be treated at home with bed rest, analgesics, stool softeners, and hydration. Men with acute prostatitis complicated by urinary retention are best managed with a suprapubic catheter or intermittent catheterization. Lack of clinical response to antibiotics should raise the suspicion of an abscess and prompt an imaging study such as a transrectal ultrasound (TRUS).

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.

Complications of TOA are related to the possible removal of one or both ovaries and fallopian tubes. Without these reproductive structures, fertility can be affected. Surgical complications can develop and include:

- Allergic shock due to anesthetics

- A paradoxical reaction to a drug

- Infection

A variety of drugs may be prescribed based on the cause of the patient's urethritis. Some examples of medications based on causes include: azithromycin, doxycycline, erythromycin, levofloxacin, metronidazole, ofloxacin, or tinidazole.

Proper perineal hygiene should be stressed. This includes avoiding use of vaginal deodorant sprays and proper wiping after urination and bowel movements. Intercourse should be avoided until symptoms subside.

Treatment is based on the prescription and use of the proper antibiotics depending on the strain of the ureaplasma.

Because of its multi-causative nature, initial treatment strategies involve using a broad range antibiotic that is effective against chlamydia (such as doxycycline). It is imperative that both the patient and any sexual contacts be treated. Women infected with the organisms that cause NGU may develop pelvic inflammatory disease. If symptoms persist, follow-up with a urologist may be necessary to identify the cause.

According to a study, tinidazole used with doxycycline or azithromycin may cure NGU better than when doxycycline or azithromycin is used alone.

If left untreated, complications include epididymitis and infertility. Consistent and correct use of latex condoms during sexual activity greatly reduces the likelihood of infection.

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.

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.

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.

No treatment required. It is standard practice for men with infertility and category IV prostatitis to be given a trial of antibiotics and/or anti-inflammatories, although evidence of efficacy are weak. Since signs of asymptomatic prostatic inflammation may sometimes be associated with prostate cancer, this can be addressed by tests that assess the ratio of free-to-total PSA. The results of these tests were significantly different in prostate cancer and category IV prostatitis in one study.

"C. trachomatis" infection can be effectively cured with antibiotics. Guidelines recommend azithromycin, doxycycline, erythromycin, levofloxacin or ofloxacin. Agents recommended during pregnancy include erythromycin or amoxicillin.

An option for treating sexual partners of those with chlamydia or gonorrhea include patient-delivered partner therapy (PDT or PDPT), which is the practice of treating the sex partners of index cases by providing prescriptions or medications to the patient to take to his/her partner without the health care provider first examining the partner.

Following treatment people should be tested again after three months to check for reinfection.

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.

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.

Risk of some causes of urethritis can be lessened by avoiding unprotected sexual activity, chemicals that could irritate the urethra; this could include detergents or lotions as well as spermicides or contraceptives, and irritation caused by manual manipulation of the urethra.

Treatment involves a course of antibiotics to cover the appropriate organisms, typically ceftriaxone plus azithromycin. Laparoscopy for lysis of adhesions may be performed for refractory pain.

It is recommended that sexual partners be tested and potentially treated. One option for treating sexual partners of people infected is patient-delivered partner therapy (PDPT), which involves providing prescriptions or medications to the person to take to his/her partner without the health care provider's first examining him/her.

The United States' Centers for Disease Control and Prevention (CDC) currently recommend that individuals who have been diagnosed and treated for gonorrhea avoid sexual contact with others until at least one week past the final day of treatment in order to prevent the spread of the bacterium.

With the advent of IVF which bypasses the need for tubal function a more successful treatment approach has become available for women who want to conceive. IVF has now become the major treatment for women with hydrosalpinx to achieve a pregnancy.

Several studies have shown that IVF patients with untreated hydrosalpinx have lower conception rates than controls and it has been speculated that the tubal fluid that enters the endometrial cavity alters the local environment or affects the embryo in a detrimental way. Thus, many specialists advocate that prior to an IVF attempt, the hydrosalpinx should be removed.

As of 2010, injectable ceftriaxone is one of the few effective antibiotics. This is typically given in combination with either azithromycin or doxycycline. As of 2015 and 2016 the CDC and WHO only recommends both ceftriaxone and azithromycin. Because of increasing rates of antibiotic resistance local susceptibility patterns must be taken into account when deciding on treatment.

For most of the past century patients with tubal infertility due to hydrosalpinx underwent tubal corrective surgery to open up the distally occluded end of the tubes (salpingostomy) and remove adhesions (adhesiolysis). Unfortunately, pregnancy rates tended to be low as the infection process often had permanently damaged the tubes, and in many cases hydrosalpinges and adhesions formed again. Further, ectopic pregnancy is a typical complication. Surgical interventions can be done by laparotomy or laparoscopy.

Non-infertile patients who suffer from severe chronic pain due to hydrosalpinx formation that is not relieved by pain management may consider surgical removal of the affected tube(s) (salpingectomy) or even a hysterectomy with removal of the tubes, possibly ovaries.

Antibiotics have been used to prevent and treat these infections however the misuse of antibiotics is a serious problem for global health. It is recommended that guidelines be followed which outline when it is appropriate to give antibiotics and which antibiotics are most effective.

Atelectasis: mild to moderate fever, no changes or mild rales on chest auscultation.

Management: pulmonary exercises, ambulation (deep breathing and walking)

Urinary tract infection : high fever, malaise, costovertebral tenderness, positive urine culture.

Management: antibiotics as per culture sensitivity (cephalosporine).

Endometritis: moderate fever, exquisite uterine tenderness, minimal abdominal findings.

Management: multiple agent IV antibiotics to cover polymicrobial organisms: clindamycin, gentamicin, addition of ampicillin if no response, no cultures are necessary.

Wound infection: persistent spiking fever despite antibiotics, wound erythema or fluctuance, wound drainage.

Management: antibiotics for cellulitis, open and drain wound, saline-soaked packing twice a day, secondary closure.

Septic pelvic thrombophlebitis: persistent wide fever swings despite antibiotics, usually normal abdominal or pelvic exams.

Management: IV heparin for 7–10 days at rates sufficient to prolong the PTT to double the baseline values.

Mastitis: unilateral, localized erythema, edema, tenderness.

Management: antibiotics for cellulitis, open and drain abscess if present.

Hematometra is usually treated by surgical cervical dilation to drain the blood from the uterus. Other treatments target the underlying cause of the hematometra; for example, a hysteroscopy may be required to resect adhesions that have developed following a previous surgery. If the cause of the hematometra is unclear, a biopsy of endometrial tissue can be taken to test for the presence of a neoplasm (cancer). Antibiotics may be given as prophylaxis against the possibility of infection.

It has been suggested that suction drains placed during surgery and non-peritonisation (not closing the posterior peritoneum) may reduce the possibility of lymphocele development.

Smaller lymphoceles can be managed expectantly, and many lesions will regress over time. For symptomatic lesions a number of approaches are available and include fine needle aspiration with US or CT guidance, catheter insertion and drainage (with possible use of sclerosants), and surgical drainage. Sex and masturbation may cause the lymphocele to grow if it is in the genital area. It is suggested to avoid these activities for around one to one and a half months. Some exercises may also help to shrink it.

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.

For fallopian tube obstruction, alternative medicine has been used as a form of fertility treatment. A study of the use of alternative methods showed that only a minority of infertile couples utilize such treatments. It also showed that alternative methods are more often chosen by couples who were wealthier, have not yet achieved pregnancy, or had a belief in the effectiveness of such treatments. Of the study participants, 29% used a CAM modality for treatment, 22% used acupuncture, 17% used herbal therapies like Fuyan Pill, and 1% using meditation.