One of the most common causes of rectal pain is an anal fissure. It involves a tear in the anal canal probably due to trauma from defecation and are usually treated effectively with sitz baths, stool softeners, and analgesics.

Two more highly common causes of functional anorectal pain are levator ani syndrome (LAS) and proctalgia fugax. Both of these conditions are thought to be caused by muscle spasms of the either the levator ani muscle or the anal sphincter muscle respectively, and may overlap symptomatically with a third less-common condition called coccygodynia which is the result of previous trauma to the coccyx bone. Stress, prolonged sitting, and constipation all seem to be associated with LAS. The majority (90%) of those reporting chronic episodes of such pain are women. Some researchers group these conditions under the medical category of "tension myalgia of the pelvic floor". Less than a third of those experiencing these conditions seek medical treatment for them. Treatment can involve the use of antispasmotic medications as well as the down-training (conscious involvement and relaxation of previously unconscious muscle movements) so that spasms occur less frequently or not at all.

Proctalgia fugax (a variant of levator ani syndrome) is a severe, episodic pain in the regions of the rectum and anus. It can be caused by cramp of the levator ani muscle, particularly in the pubococcygeal part.

It most often occurs in the middle of the night and lasts from seconds to minutes, an indicator for the differential diagnosis of levator ani syndrome, which presents as pain and aching lasting twenty minutes or longer. In a study published in 2007 involving 1809 patients, the attacks occurred in the daytime (33 per cent) as well as at night (33 per cent) and the average number of attacks was 13. Onset can be in childhood; however, in multiple studies the average age of onset was 45. Many studies showed that women are affected more commonly than men. This can be at least partly explained by men's reluctance to seek medical advice concerning such a delicate case as rectal pain.

During an episode, the patient feels spasm-like, sometimes excruciating, pain in the anus, often misinterpreted as a need to defecate. The pain must arise de novo, that is in absence of clear cause. As such, pain associated with penetrative anal intercourse, trauma or rectal foreign body insertion preclude a diagnosis of proctalgia fugax. Simultaneous stimulation of the local autonomic system can cause erection in males. In some people, twinges sometimes occur shortly after orgasm. Because of the high incidence of internal anal sphincter thickening with the disorder, it is thought to be a disorder of the internal anal sphincter or that it is a neuralgia of pudendal nerves. It is recurrent and there is also no known cure. However, some studies show effective use of botulinum toxin, pudendal nerve block, and calcium channel blockers. It is not known to be linked to any disease process and data on the number of people afflicted vary, but prevalence may be as high as 8–18%. It is thought that only 17–20% of sufferers consult a physician, so obtaining accurate data on occurrence presents a challenge.

The pain episode subsides by itself as the spasm disappears on its own, but may reoccur.

Terms such as "functional colonic disease" (or "functional bowel disorder") refer in medicine to a group of bowel disorders which are characterised by chronic abdominal complaints without a structural or biochemical cause that could explain symptoms. Other "functional" disorders relate to other aspects of the process of digestion.

The consensus review process of meetings and publications organised by the Rome Foundation, known as the Rome process, has helped to define the functional gastrointestinal disorders. Successively, the Rome I, Rome II, Rome III and Rome IV proposed consensual classification system and terminology, as recommended by the Rome Coordinating Committee. These now include classifications appropriate for adults, children and neonates / toddlers.

The current Rome IV classification, published in 2016, is as follows:

A. Esophageal Disorders

- A1. Functional chest pain

- A2. Functional heartburn

- A3. Reflux hypersensitivity

- A4. Globus

- A5. Functional dysphagia

B. Gastroduodenal Disorders

- B1. Functional dyspepsia

- B1a. Postprandial distress syndrome (PDS)

- B1b. Epigastric pain syndrome (EPS)

- B2. Belching disorders

- B2a. Excessive supragastric belching

- B2b. Excessive gastric belching

- B3. Nausea and vomiting disorders

- B3a. Chronic nausea vomiting syndrome (CNVS}

- B3b. Cyclic vomiting syndrome (CVS)

- B3c. Cannabinoid hyperemesis syndrome (CHS)

- B4. Rumination syndrome

C. Bowel Disorders

- C1. Irritable bowel syndrome (IBS)

- IBS with predominant constipation (IBS-C)

- IBS with predominant diarrhea (IBS-D)

- IBS with mixed bowel habits (IBS-M)

- IBS unclassified (IBS-U)

- C2. Functional constipation

- C3. Functional diarrhea

- C4. Functional abdominal bloating/distension

- C5. Unspecified functional bowel disorder

- C6. Opioid-induced constipation

D. Centrally Mediated Disorders of Gastrointestinal Pain

- D1. Centrally mediated abdominal pain syndrome (CAPS)

- D2. Narcotic bowel syndrome (NBS)/ Opioid-induced GI hyperalgesia

E. Gallbladder and Sphincter of Oddi disorders

- E1. Biliary pain

- E1a. Functional gallbladder disorder

- E1b. Functional biliary sphincter of Oddi disorder

- E2. Functional pancreatic sphincter of Oddi disorder

F. Anorectal Disorders

- F1. Fecal incontinence

- F2. Functional anorectal pain

- F2a. Levator ani syndrome

- F2b. Unspecified functional anorectal pain

- F2c. Proctalgia fugax

- F3. Functional defecation disorders

- F3a. Inadequate defecatory propulsion

- F3b. Dyssynergic defecation

G. Childhood Functional GI Disorders: Neonate/Toddler

- G1. Infant regurgitation

- G2. Rumination syndrome

- G3. Cyclic vomiting syndrome (CVS)

- G4. Infant colic

- G5. Functional diarrhea

- G6. Infant dyschezia

- G7. Functional constipation

H. Childhood Functional GI Disorders: Child/Adolescent

- H1. Functional nausea and vomiting disorders

- H1a. Cyclic vomiting syndrome (CVS)

- H1b. Functional nausea and functional vomiting

- H1b1. Functional nausea

- H1b2. Functional vomiting

- H1c. Rumination syndrome

- H1d. Aerophagia

- H2. Functional abdominal pain disorders

- H2a. Functional dyspepsia

- H2a1. Postprandial distress syndrome

- H2a2. Epigastric pain syndrome

- H2b. Irritable bowel syndrome (IBS)

- H2c. Abdominal migraine

- H2d. Functional abdominal pain ‒ NOS

- H3. Functional defecation disorders

- H3a. Functional constipation

- H3b. Nonretentive fecal incontinence

Functional gastrointestinal disorders are very common. Globally, irritable bowel syndrome and functional dyspepsia alone may affect 16–26% of the population.