These may reveal congestion and edema (swelling) of the distal rectal mucosa, and in 10-15% of cases there may be a solitary rectal ulcer on the anterior rectal wall. Localized inflammation or ulceration can be biopsied, and may lead to a diagnosis of SRUS or colitis cystica profunda. Rarely, a neoplasm (tumour) may form on the leading edge of the intussusceptum. In addition, patients are frequently elderly and therefore have increased incidence of colorectal cancer. Full length colonoscopy is usually carried out in adults prior to any surgical intervention. These investigations may be used with contrast media (barium enema) which may show the associated mucosal abnormalities.

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.

Various modalities of diagnosis are available:

- Cystoscopy

- Colonoscopy

- Poppy seed test

- Transabdominal ultrasonography

- Abdominopelvic CT

- MRI

- Barium enema

- Bourne test

- Cystogram

A definite algorithm of tests is followed for making the diagnosis.

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.

Diet and lifestyle are believed to play a large role in whether colorectal polyps form. Studies show there to be a protective link between consumption of cooked green vegetables, brown rice, legumes, and dried fruit and decreased incidence of colorectal polyps.

Colostomy is recommended by most surgeons, and has a good prognosis, with 90% of patients regaining normal bowel control. Since the rectal opening and anal orifice in a vestibular fistula tend to be short and narrow, a colostomy is usually performed to allow decompression of the bowel unless the orifice is wide enough to allow normal defecation. Colostomy is often followed by posterior sagittal anorectoplasty (PSARP), a surgical procedure to repair the anal orifice, at a later date. Some surgeons prefer to perform an immediate PSARP without a colostomy first, while others perform neither a colostomy nor a PSARP and instead opt for a simple dilatation of the orifice to allow stool to pass and the bowel to decompress. It has been suggested that only experienced surgeons should perform repair without an initial colostomy.

Imperforate anus usually requires immediate surgery to open a passage for feces unless a fistula can be relied on until corrective surgery takes place. Depending on the severity of the imperforate, it is treated either with a perineal anoplasty or with a colostomy.

While many surgical techniques to definitively repair anorectal malformations have been described. The posterior sagittal approach (PSARP) has become the most popular. It involves dissection of the perineum without entry into the abdomen and 90% of defects in boys can be repaired this way.

After diagnosing rectovaginal fistula, it is best to wait for around 3 months to allow the inflammation to subside. For low fistulae, a vaginal approach is best, while an abdominal repair would be necessary for a high fistula at the posterior fornix.

A circular incision is made around the fistula and vagina is separated from the underlying rectum with a sharp circumferential dissection. The entire fistulous tract, along with a small rim of rectal mucosa is incised. The rectal wall is then closed extramucosally.

Most rectovaginal fistuals will need surgery to fix. Medications such as antibiotics and Infliximab might be prescribed to help close the rectovaginal fistula or prepare for surgery.

The prognostic outcomes for this type of cloaca are good for bowel control and urinary function. The surgical repair for this type of cloaca can usually be done by performing posterior sagittal approach without opening of the abdomen. A common channel longer than 3 cm in length usually has poor sphincter muscles and a poor sacrum, suggesting a prognostic outcome for bowel control and urinary function to be less likely. Common channels longer than 3 cm are generally considered more complex and more technically challenging in surgical repair.

With a high lesion, many children have problems controlling bowel function and most also become constipated. With a low lesion, children generally have good bowel control, but they may still become constipated.

For children who have a poor outcome for continence and constipation from the initial surgery, further surgery to better establish the angle between the anus and the rectum may improve continence and, for those with a large rectum, surgery to remove that dilated segment may significantly improve the bowel control for the patient. An antegrade enema mechanism can be established by joining the appendix to the skin (Malone stoma); however, establishing more normal anatomy is the priority.

The diagnosis of a rectovestibular fistula can be made in female newborns if the vulva is stained with meconium (the earliest form of stool in an infant). The opening of the anus may be difficult to see due to its small size and position, but it may be visible as a thickening of the median perineal raphe with an obvious anal dimple. Patients with rectovestibular fistulae are commonly misdiagnosed with rectovaginal fistulae.

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

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.

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.

Colorectal polyps can be detected using a faecal occult blood test, flexible sigmoidoscopy, colonoscopy, virtual colonoscopy, digital rectal examination, barium enema or a pill camera.

Malignant potential is associated with

- degree of dysplasia

- Type of polyp (e.g. villous adenoma):

- Tubular Adenoma: 5% risk of cancer

- Tubulovillous adenoma: 20% risk of cancer

- Villous adenoma: 40% risk of cancer

- Size of polyp:

- <1 cm =<1% risk of cancer

- 1 cm=10% risk of cancer

- 2 cm=15% risk of cancer

Normally an adenoma which is greater than 0.5 cm is treated

Diagnosis of a female with cloaca should be suspected in a female born with an imperforate anus and small looking genitalia. The diagnosis can be made clinically. Failure to identify a cloaca as being present in a newborn may be dangerous, as more than 90% have associated urological problems. The goal for treatment of a female born with cloaca is to achieve bowel control, urinary control, and sexual function, which includes menstruation, sexual intercourse, and possibly pregnancy. Cloacas probably occur in 1 in 20,000 live births.

Rectovaginal fistulas are often the result of trauma during childbirth (in which case it is known as obstetric fistula) where improper medical interventions are used, such as episiotomy with forceps/vacuum extraction or in situations where there is inadequate health care, such as in some developing countries. Rectovaginal fistula is said to be known as the leading cause in maternal death in developing countries. Risk factors include prolonged labour, difficult instrumental delivery and paramedian episiotomy. Rates in Eritrea are estimated as high as 350 per 100,000 vaginal births. Fistulas can also develop as a result of physical trauma to either the vagina or anus, including from rape. Women with rectovaginal fistulae are often stigmatized in developing countries, and become outcasts.

Rectovaginal fistula can also be a symptom of various diseases, including infection by lymphogranuloma venereum, or the unintended result of surgery, such as episiotomy or sexual reassignment surgery. They may present as a complication of vaginal surgery, including vaginal hysterectomy. They are a recognized presentation of rectal carcinoma or rarely diverticular disease of the bowel or Crohn's disease. They are seen rarely after radiotherapy treatment for cervical cancer.

Diagnosis is achieved mainly by plain and contrasted radiographical and ultrasound imaging. Colonic marker transit studies are useful to distinguish colonic inertia from functional outlet obstruction causes. In this test, the patient swallows a water-soluble bolus of radio-opaque contrast and films are obtained 1, 3 and 5 days later. Patients with colonic inertia show the marker spread throughout the large intestines, while patients with outlet obstruction exhibit slow accumulations of markers in some places. A colonoscopy can also be used to rule out mechanical obstructive causes. Anorectal manometry may help to differentiate acquired from congenital forms. Rectal biopsy is recommended to make a final diagnosis of Hirschsprung disease.

Because of the way familial polyposis develops, it is possible to have the genetic condition, and therefore be at risk, but have no polyps or issues so far. Therefore, an individual may be diagnosed "at risk of" FAP, and require routine monitoring, but not (yet) actually have FAP (i.e., carries a defective gene but as yet appears not to have any actual medical issue as a result of this). Clinical management can cover several areas:

- Identifying those individuals who could be at risk of FAP: usually from family medical history or genetic testing

- Diagnosis (confirming whether they have FAP)—this can be done either by genetic testing, which is definitive, or by visually checking the intestinal tract itself.

- Screening / monitoring programs involve visually examining the intestinal tract to check its healthy condition. It is undertaken as a routine matter every few years where there is cause for concern, when either (a) a genetic test has confirmed the risk or (b) a genetic test has not been undertaken for any reason so the actual risk is unknown. Screening and monitoring allows polyposis to be detected visually before it can become life-threatening.

- Treatment, typically surgery of some kind, is involved if polyposis has led to a large number of polyps, or a significant risk of cancer, or actual cancer.

Doctors uses a variety of tools and techniques to evaluate the type of anorectal disorder, including digital and anoscopic investigations, palpations, and palpitations. The initial examination can be painful because a gastroenterologist will need to spread the buttocks and probe the painful area, which may require a local anesthetic.

Monitoring involves the provision of outpatient colonoscopy, and occasionally upper gastric tract esophagogastroduodenoscopy (EGD, to search for premalignant gastric or duodenal tumors), typically once every 1–3 years, and/or a genetic blood test to definitively confirm or deny susceptibility. A small number of polyps can often be excised (removed) during the procedure, if found, but if there are more severe signs or numbers, in patient surgery may be required.

NCBI states that when an individual is identified as having FAP, or the mutations resulting in FAP: "It is appropriate to evaluate the parents of an affected individual (a) with molecular genetic testing of APC if the disease-causing mutation is known in the proband [person first identified with the condition] or (b) for clinical manifestations of APC-associated polyposis conditions".

If fecal matter passes through the fistula into the bladder, the existence of the fistula may be revealed by pneumaturia or fecaluria.

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

Anorectal anomalies are medical problems affecting the structure of the anus and rectum. A person with an anorectal problem would have some sort of deformative feature of the anus or rectum, collectively known as an anorectal malformation.

Examples of anorectal anomalies include:

- Anal stenosis

- Imperforate anus

- Proctitis

- Anal bleeding

- Anal fistula

- Anal cancer

- Anal itching

- Hemorrhoid (piles)

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.