To properly diagnose the extent of prostate cancer, the urologist will usually want to do a biopsy. This involves cutting a piece of the tissue in order to closely examine it for cancer cells. The prostate biopsy procedure can be done in a number of ways, but the end result is with a spring-loaded needle entering the prostate and taking about a dozen samples. Obviously, this can get a bit uncomfortable, but is usually done as an outpatient procedure. The three main routes of biopsy are through the rectum, the perineum, or the urethra.

First, the doctor will apply either local or general anesthetic. General anesthetic is generally associated with a longer hospital stay. Antibiotics are also usually given, especially if the needle is to be inserted through the rectum, to keep fecal matter from infecting the patient.

Also, usually a rectal ultrasound will be used to guide the urologist. If going the route of the urethra, the doctor will insert a cytoscope (a lighted instrument) into the urethra for guidance. If by perineum, the doctor will first cut a small incision. And if by rectum, the doctor will sometimes use a finger-guided needle.

After maneuvering the needle to the prostate gland, he will the take 6 to 12 small samples from the prostate, usually from both sides. This can be a bit painful as the needle pierces the prostate.

The procedure usually takes about 30 minutes (varying depending on the route used), and after effects may include blood in the urine, feces, and semen for several days afterward.

The prostate biopsy procedure will usually only result in about 1% of the prostate being sampled, and so false negatives can result as cancer can be hiding elsewhere. In addition to a biopsy, other methods will be combined to get a more complete picture, such as measuring PSA levels.

The urologist will then take the prostate samples, look for the two most common cell types (whether cancer or prostate cells), assign them a scale from 1 to 5, and add them together to get the Gleason Score, which indicates prognosis.