Pelvic floor dysfunction can be diagnosed by history and physical exam, though it is more accurately graded by imaging. Historically, fluoroscopy with defecography and cystography were used, though modern imaging allows the usage of MRI to complement and sometimes replace fluoroscopic assessment of the disorder, allowing for less radiation exposure and increased patient comfort, though an enema is required the evening before the procedure. Instead of contrast, ultrasound gel is used during the procedure with MRI. Both methods assess the pelvic floor at rest and maximum strain using coronal and sagittal views. When grading individual organ prolapse, the rectum, bladder and uterus are individually assessed, with prolapse of the rectum referred to as a rectocele, bladder prolapse through the anterior vaginal wall a cystocele, and small bowel an enterocele.

To assess the degree of dysfunction, three measurements must be taken into account. First, an anatomic landmark known as the pubococcygeal line must be determined, which is a straight line connecting the inferior margin of the pubic symphysis at the midline with the junction of the first and second coccygeal elements on a sagittal image. After this, the location of the puborectalis muscle sling is assessed, and a perpendicular line between the pubococcygeal line and muscle sling is drawn. This provides a measurement of "pelvic floor descent", with descent greater than 2 cm being considered mild, and 6 cm being considered severe. Lastly, a line from the pubic symphysis to the puborectalis muscle sling is drawn, which is a measurement of the pelvic floor hiatus. Measurements of greater than 6 cm are considered mild, and greater than 10 cm severe. The degree of organ prolapse is assessed relative to the hiatus. The grading of "organ prolapse" relative to the hiatus is more strict, with any descent being considered abnormal, and greater than 4 cm being considered severe.

This investigation is used to diagnose internal intussusception, or demonstrate a suspected external prolapse that could not be produced during the examination. It is usually not necessary with obvious external rectal prolapse. Defecography may demonstrate associated conditions like cystocele, vaginal vault prolapse or enterocele.

Identification of the exact causes usually begins with a thorough medical history, including detailed questioning about symptoms, bowel habits, diet, medication and other medical problems. Digital rectal examination is performed to assesses resting pressure and voluntary contraction (maximum squeeze) of the sphincter complex and puborectalis. Anal sphincter defects, rectal prolapse, and abnormal perineal descent may be detected. Anorectal physiology tests assess the functioning of the anorectal anatomy. Anorectal manometry records the pressure exerted by the anal sphincters and puborectalis during rest and during contraction. The procedure is also able to assess sensitivity of the anal canal and rectum. Anal electromyography tests for nerve damage, which is often associated with obstetric injury. Pudendal nerve terminal motor latency tests for damage to the pudendal motor nerves. Proctography, also known as defecography, shows how much stool the rectum can hold, how well the rectum holds it, and how well the rectum can evacuate the stool. It will also highlight defects in the structure of the rectum such as internal rectal intussusception. Dynamic pelvic MRI, also called MRI defecography is an alternative which is better for some problems but not as good for other problems. Proctosigmoidoscopy involves the insertion of an endoscope (a long, thin, flexible tube with a camera) into the anal canal, rectum and sigmoid colon. The procedure allows for visualization of the interior of the gut, and may detect signs of disease or other problems that could be a cause, such as inflammation, tumors, or scar tissue. Endoanal ultrasound, which some consider to be the gold standard for detection of anal canal lesions, evaluates the structure of the anal sphincters, and may detect occult sphincter tears that otherwise would go unseen.

Functional FI is common. The Rome process published diagnostic criteria for functional FI, which they defined as "recurrent uncontrolled passage of fecal material in an individual with a developmental age of at least 4 years". The diagnostic criteria are, one or more of the following factors present for the last 3 months: abnormal functioning of normally innervated and structurally intact muscles, minor abnormalities of sphincter structure/innervation (nerve supply), normal or disordered bowel habits, (i.e., fecal retention or diarrhea), and psychological causes. Furthermore, exclusion criteria are given. These are factors which all must be excluded for a diagnosis of functional FI, and are abnormal innervation caused by lesion(s) within the brain (e.g., dementia), spinal cord (at or below T12), or sacral nerve roots, or mixed lesions (e.g., multiple sclerosis), or as part of a generalized peripheral or autonomic neuropathy (e.g., due to diabetes), anal sphincter abnormalities associated with a multisystem disease (e.g., scleroderma), and structural or neurogenic abnormalities that are the major cause.

Colonic transit studies may be used to rule out colonic inertia if there is a history of severe constipation. Continent prolapse patients with slow transit constipation, and who are fit for surgery may benefit from subtotal colectomy with rectopexy.

Several severity scales exist. The Cleveland Clinic (Wexner) fecal incontinence score takes into account five parameters that are scored on a scale from zero (absent) to four (daily) frequency of incontinence to gas, liquid, solid, of need to wear pad, and of lifestyle changes. The Park's incontinence score uses four categories:

The fecal incontinence severity index is based on four types of leakage (gas, mucus, liquid stool, solid stool) and five frequencies (once to three times per month, once per week, twice per week, once per day, twice or more per day). Other severity scales include: AMS, Pescatori, Williams score, Kirwan, Miller score, Saint Mark's score and the Vaizey scale.

Physical examination can rule out anismus (by identifying another cause) but is not sufficient to diagnose anismus.

The rectal cooling test is suggested to differentiate between rectal inertia and impaired relaxation/paradoxical contraction

Other techniques include manometry, balloon expulsion test, evacuation proctography (see defecating proctogram), and MRI defecography. Diagnostic criteria are: fulfillment of criteria for functional constipation, manometric and/or EMG and/or radiological evidence (2 out of 3), evidence of adequate expulsion force, and evidence of incomplete evacuation. Recent dynamic imaging studies have shown that in persons diagnosed with anismus the anorectal angle during attempted defecation is abnormal, and this is due to abnormal (paradoxical) movement of the puborectalis muscle.

Treatment depends on the severity of the problem, and may include non-surgical methods such as changes in diet (increase in fiber and water intake), pelvic floor exercises such as Kegel exercises, use of stool softeners, hormone replacement therapy for post-menopausal women and insertion of a pessary into the vagina. A high fiber diet, consisting of 25-30 grams of fiber daily, as well as increased water intake (typically 6-8 glasses daily), help to avoid constipation and straining with bowel movements, and can relieve symptoms of rectocele.

Cystoceles are treated with a surgical procedure known as a Burch colposuspension, with the goal of suspending the prolapsed urethra so that the urethrovesical junction and proximal urethra are replaced in the pelvic cavity. Uteroceles are treated with hysterectomy and uterosacral suspension. With enteroceles, the prolapsed small bowel is elevated into the pelvis cavity and the rectovaginal fascia is reapproximated. Rectoceles, in which the anterior wall of the rectum protrudes into the posterior wall of the vagina, require posterior colporrhaphy.

Surgery can be done to correct rectocele when symptoms continue despite the use of non-surgical management, and are significant enough to interfere with activities of daily living.

Surgery to correct the rectocele may involve the reattachment of the muscles that previously supported the pelvic floor. Another procedure is posterior colporrhaphy, which involves suturing of vaginal tissue. Surgery may also involve insertion of a supporting mesh (that is, a patch). There are also surgical techniques directed at repairing or strengthening the rectovaginal septum, rather than simple excision or plication of vaginal skin which provides no support. Both gynecologists and colorectal surgeons can address this problem. Potential complications of surgical correction of a rectocele include bleeding, infection, dyspareunia (pain during intercourse), as well as recurrence or even worsening of the rectocele symptoms. The use of synthetic or biologic grafts has been questioned.

Vaginal prolapses are treated according to the severity of symptoms. They can be treated:

- With conservative measures (changes in diet and fitness, Kegel exercises, pelvic floor physical therapy.

- With a pessary, a rubber or silicon device fitted to the patient which is inserted into the vagina and may be retained for up to several months. Pessaries are a good choice of treatment for women who wish to maintain fertility, are poor surgical candidates, or who may not be able to attend physical therapy. Pessaries require a provider to fit the device, but most can be removed, cleaned, and replaced by the woman herself. Pessaries should be offered to women considering surgery as a non-surgical alternative.

- With surgery (for example native tissue repair, biological graft repair, absorbable and non-absorbable mesh repair, colpopexy, colpocleisis). Surgery is used to treat symptoms such as bowel or urinary problems, pain, or a prolapse sensation. According to the Cochrane Collaboration review (2016) current evidence does not support the use of transvaginal surgical mesh repair compared with native tissue repair for anterior compartment prolapse owing to increased morbidity. Safety and efficacy of many newer meshes is unknown. The use of a transvaginal mesh in treating vaginal prolapses is associated with side effects including pain, infection, and organ perforation. According to the FDA, serious complications are "not rare." A number of class action lawsuits have been filed and settled against several manufacturers of TVM devices.

Diagnosis is by rectal examination. A specialized tool called a "Perineocaliper" can be used to measure the descent of the perineum. A retro anal ultrasound scan may demonstrate the condition. "Anti sagging tests", whereby the abnormal descent is corrected temporarily, may help to show whether symptoms are due to descending perineum syndrome or are in fact due to another condition.

Normally, the anal margin lies just below a line drawn between the coccyx (tailbone) and the pubic symphysis. In descending perineum syndrome the anal canal is situated several cm below this imaginary line, or it descends 3–4 cm during straining.

Defecography may also demonstrate abnormal perineal descent.

Obstructed defecation has many causes, so the management in any individual case is specific to the cause of the symptom. For rectal internal intususception treatment is surgical, either STARR or rectopexy. For rectocele STARR or mesh implantation. For anismus/ pelvic floor dessynergia: biofeedback exercise.

Genital prolapse occurs in about 316 million women worldwide as of 2010 (9.3% of all females).

The two key features of obstructed defecation are:

1. An inability to voluntarily evacuate rectal contents

2. Normal colonic transit time

A 5 item questionnaire was validated for diagnosis and grading of obstructed defecation syndrome. The parameters were:

1. Excessive straining

2. Incomplete rectal evacuation

3. Use of enemas and/or laxatives

4. Vaginal-anal-perineal digitations (needing to press in the back wall of the vagina or on the perineum to aid defecation)

5. Abdominal discomfort and/or pain

Surgical treatments may be used to treat the condition, and include retro-rectal levatorplasty, post-anal repair, retro-anal levator plate myorrhaphy.

Mucus coats the walls of the colon in health, functioning as a protective barrier and also to aid peristalsis by lubrication of stool. Mucous discharges can be thought of in three broad categories:

- Normal physiologically produced mucus

- Inappropriately expressed physiologically produced mucus (e.g. in the presence of sphincter defects, or lesions preventing normal sphincter closure, allowing seepage or soiling)

- Mucus produced in pathological quantities (e.g. from a lesion, or generalized coloproctitis or as a result of bacterial overgrowth)

A mucous rectal discharge may be blood-streaked. With some conditions, the blood can be homogenously mixed with the mucus, creating a pink goo. An example of this could be the so-called "red currant jelly" stools in intussusception. This appearance refers to the mixture of sloughed mucosa, mucus, and blood.

Note: "mucus" is a noun, used to name the substance itself, and "mucous" is an adjective, used to describe a discharge. "Mucoid" is also an adjective and means mucus-like. "Mucinous" strictly speaking refers to something having a mucin-like attribute, but it often is used interchangeably with the word "mucous" (as mucus usually contains a high percentage of mucin).

Several pathologies can present with perianal discharge. Although not exactly the same as rectal discharge, perianal discharge can be misinterpreted as such, given the anatomical proximity.

Fistulae draining into the perianal region, as well as pilonidal diseases, are the main entities that fall within this category. Perianal tumours can also discharge when they fungate, or otherwise become cystic or necrotic.

The main diagnostic tools are blood tests, X-rays of the abdomen, CT scanning, and/or ultrasound. If a mass is identified, biopsy may determine the nature of the mass.

Radiological signs of bowel obstruction include bowel distension and the presence of multiple (more than six) gas-fluid levels on supine and erect abdominal radiographs.

Contrast enema or small bowel series or CT scan can be used to define the level of obstruction, whether the obstruction is partial or complete, and to help define the cause of the obstruction.

According to a meta-analysis of prospective studies by the Cochrane Collaboration, the appearance of water-soluble contrast in the cecum on an abdominal radiograph within 24 hours of oral administration predicts resolution of an adhesive small bowel obstruction with a pooled sensitivity of 97% and specificity of 96%.

Colonoscopy, small bowel investigation with ingested camera or push endoscopy, and laparoscopy are other diagnostic options.

Fetal and neonatal bowel obstructions are often caused by an intestinal atresia, where there is a narrowing or absence of a part of the intestine. These atresias are often discovered before birth via an ultrasound, and treated with using laparotomy after birth. If the area affected is small, then the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for a period of time, a temporary stoma may be placed.