Anal Canal Anatomy

The anal canal is the most terminal part of the lower GI tract/large intestine, which lies between the anal verge (anal orifice, anus) in the perineum below and the rectum above. The description in this topic is from below upwards, as that is how this region is usually examined in clinical practice. Images depicting the anal canal can be seen below. 

The anal canal is completely extraperitoneal. The length of the anal canal is about 4 cm (range, 3-5 cm), with two thirds of this being above the pectinate line (also known as the dentate line) and one third below the pectinate line.

The epithelium of the anal canal between the anal verge below and the pectinate line above is variously described as anal mucosa or anal skin. The author believes that it should be called anal skin (anoderm), as it looks like (pigmented) skin, is sensitive like skin (why a fissure-in-ano is very painful), and is keratinized (but does not have skin appendages).

The pectinate line is the site of transition of the proctodeum below and the postallantoic gut above. It is a scalloped demarcation formed by the anal valves (transverse folds of mucosa) at the inferior-most ends of the anal columns. Anal glands open above the anal valves into the anal sinuses. The pectinate line is not seen on inspection in clinical practice, but under anesthesia the anal canal descends down, and the pectinate line can be seen on slight retraction of the anal canal skin.

Blood supply and lymphatics

The anal canal above the pectinate line is supplied by the terminal branches of the superior rectal (hemorrhoidal) artery, which is the terminal branch of the inferior mesenteric artery. The middle rectal artery (a branch of the internal iliac artery) and the inferior rectal artery (a branch of the internal pudendal artery) supply the lower anal canal.


Anorectal sphincter tone can be assessed during digital rectal examination (DRE) when the patient is asked to squeeze the examining finger. Anorectal manometry measures the pressures: resting and squeezing.


The anal canal below the pectinate line develops from the proctodeum (ectoderm), while that above the pectinate line develops from the endoderm of the hindgut.

Best Pathology lab in Pune

The perianal skin is keratinized, stratified squamous epithelium with skin appendages (eg, hair, sweat glands, sebaceous glands, somatic nerve endings that are sensitive to pain). The anal canal skin (anoderm) is also keratinized, stratified squamous epithelium and has somatic nerve endings (sensitive to pain), but without skin appendages. The anal canal mucosa is cuboidal in the transitional zone and columnar above it; it is insensitive to pain. The rectal mucosa above the anorectal junction is lined by pinkish red, insensitive columnar epithelium.

The anorectal flexure is formed by the puborectalis (the innermost fibers of levator ani muscle, which extends from the pubic bone, obturator fascia, and ischial spine to the coccyx and anococcygeal ligament) and the upper ends of the external and internal anal sphincters. Puborectalis plays a much more important role in continence than the internal and external sphincters. The involuntary autonomous internal anal sphincter is the lowermost continuation of the inner, circular smooth muscle layer of the rectum. The external longitudinal muscle layer continues as the corrugator cutis ani. The external anal sphincter has 3 parts: subcutaneous, superficial, and deep. The external anal sphincter is composed of skeletal muscle, is under voluntary control, and is supplied by pudendal nerves (S2-S4).

Pathophysiologic Variants

Pathophysiologic anal variants include the following:

  • Anal atresia
  • Ectopic Anus
  • Persistent Cloaca

Anal atresia (imperforate anus) is a low anorectal malformation in which the anus is either atretic (absent) or narrowed and the colon and rectum are normal. If the proctodeum and the postallantoic gut fail to unite, an imperforate anus results.

In ectopic anus, the anus is misplaced, usually anteriorly in the perineum (in males) or in the vagina (in females). Persistent cloaca is a common passage in which the lower GI tract (rectum), lower urinary tract (bladder or urethra), and lower genital tract in females (vagina) are open.

Perianal Lesions

The location of perianal lesions is described in relation to a clock (as seen in the supine position), eg, 2 o’clock, 7 o’clock. Sites of perianal lesions include the following:

  • Perianal skin – Abscess, hematoma (erroneously called thrombosed external hemorrhoids), external opening of fistula-in-ano, skin tag (in chronic fissure-in-ano)
  • Anal canal skin (anoderm, below dentate line) – Fissure-in-ano, externalhemorrhoids, cancer
  • Anal canal mucosa (above pectinate line) – Internal hemorrhoids, cancer

The pectinate line cannot be felt on rectal examination but is seen on anoproctoscopy; under anesthesia, the pectinate line can be seen on retraction of the perianal skin. The anorectal flexure can be palpated on rectal examination (but not under anesthesia when the muscles relax).

Infection of an anal gland is considered the initial event in the formation of a perianal abscess and then fistula-in-ano. Fissure-in-ano is an ulcer in the sensitive anal canal skin and is a very painful condition. Fistula-in-ano can be intersphincteric, trans-sphincteric, or suprasphincteric. The internal opening of fistula-in-ano can be in the anal canal or rectum.

External hemorrhoids are in located below the pectinate line on sensitive anal canal skin and are painful, while internal hemorrhoids are located above the pectinate line in insensitive anal canal mucosa and are painless (unless complicated). For the same reason, internal hemorrhoids can be intervened (injected with sclerosant or ligated with rubber band) without anesthesia.

During posterior or lateral sphincterotomy for fissure in ano, it is only the internal sphincter that is divided.

A cruciate incision in the perianal skin lateral to the anal verge provides easy and direct access to ischioanal fossae for drainage of an abscess.

Surgical considerations

Intersphincteric resection of the rectum (eg, for ulcerative colitis) follows the plane between the external and internal sphincters; external anal sphincter, levator ani, and puborectalis muscles are preserved.

In hand-sewn ileal pouch anal anastomosis (IPAA), also called restorative proctocolectomy (RPC) for ulcerative colitis, the ileal pouch is anastomosed to the pectinate line, which is exposed perianally. For stapled IPAA, the surgical anal canal is divided 1-2 cm above the pectinate line using a linear stapler; the ileal pouch is then anastomosed to the anal canal stump using a circular stapler.

Cancers of anal canal below the pectinate line are usually squamous cell carcinoma (or basal cell carcinoma and melanoma), whereas those of the anal canal above pectinate line (and of the rectum) are adenocarcinoma. Anal canal and low rectal cancers can infiltrate the anorectal ring and cause incontinence—a contraindication for sphincter preservation (by chemoradiotherapy for squamous cell carcinoma and low-anterior resection for adenocarcinoma). Anal canal cancer (or rectal cancer infiltrating into the anal canal) spreads to the superficial inguinal lymph nodes.

Imaging considerations

Magnetic resonance imaging (MRI) has become the imaging modality of choice for delineation of anal and perianal anatomy in diseases such as fistula-in-ano, incontinence, and anorectal cancer, among others.