Alkaptonuria is a genetic disorder, and urine that turns dark is present from birth. However, additional symptoms usually do not appear until adulthood. Symptoms are generally slowly progressive. The urine of individuals with alkaptonuria may be abnormally dark or it may turn black upon long-standing exposure to the air. However, since this change often takes several hours, it often goes unnoticed. During infancy, diapers may be stained black (from urine exposure to air), although this is often missed or ignored.

The first noticeable signs and symptoms of alkaptonuria usually do not develop until approximately 30 years of age and are due to chronic accumulation of homogentisic acid in connective tissue, especially cartilage. Affected individuals develop a condition called ochronosis, in which connective tissue such as cartilage turns blue, grey or black due to the chronic accumulation of homogentisic acid. In many individuals, cartilage within the ear may become thickened, irregular and discolored blue, grey or black. Eventually, this discoloration may be apparent on the skin overlying the cartilage. In many cases, the whites of the eyes (sclera) also become discolored. However, this pigmentation does not interfere with vision.

In addition to cartilage, homogentisic acid accumulates in other connective tissue including tendons and ligaments and even bone. Over time, affected tissue becomes discolored, brittle and weak. Affected individuals may develop abnormalities affecting the tendons including thickened Achilles tendons and inflammation of the tendons (tendonitis). Affected tendons and ligaments may be particularly susceptible to rupturing. Eventually, discoloration of tendons may become visible on the overlying skin.

Long-standing alkaptonuria leads to chronic joint pain and inflammation (arthritis), especially in the spine and large joints (ochronotic arthropathy). Arthritis can be severe and disabling. Low back pain and stiffness are common symptoms and are sometimes seen before the age of 30. Discs between the vertebrae flatten and calcify. Eventually, vertebrae or other bones may fuse causing stiffening or immobility of affected joints (ankylosis). Spinal involvement may lead to abnormal outward curvature of the spine causing hunching of the back (kyphosis) and loss of height. The hip, knees and shoulders are commonly affected as well. Joint mobility is usually diminished and fluid buildup in affected joints (effusions) may also occur. Joint abnormalities are progressive and may eventually necessitate a joint replacement. Joint disease in alkaptonuria tends to begin earlier and progress more rapidly in males than females.

Less often, additional symptoms may occur in alkaptonuria. Although these symptoms occur less often than the main symptoms of alkaptonuria, they occur with greater frequency than would be expected in the general population. Such symptoms include kidney stones, which develop in 50 percent of affected individuals over 64 years of age. Men with alkaptonuria may also develop prostate stones. Passage of these black stones can be extremely painful.

In some individuals, heart disease may develop due to the accumulation of homogentisic acid within the aortic or mitral valves. This accumulation causes thickening of the valves and narrowing (stenosis) of the openings of the valves. Occasionally, the narrowing is severe enough that the aortic valve needs to be replaced. The aortic valve connects the lower left chamber (main pumping chamber) of the heart with the aorta (the main artery of the body). The mitral valve is located between the left upper and left lower chambers of the heart. Affected individuals may develop calcification of the valves and/or backflow of blood back through the affected valves (regurgitation), which can lead to reduced blood flow throughout the body. Widening (dilation) of the aorta may also occur. In some cases, calcification of the small blood vessels that supply blood and oxygen to the heart (coronary blood vessels) may also occur.

Alkaptonuria does not cause developmental delays or cognitive impairment and does not appear to affect life span. However, chronic pain and mobility issues can develop.