Alkaptonuria is a very rare genetic disorder, characterized by a lack of homogentisate dioxygenase and causes accumulation of homogentisic acid. Clinical manifestations include dark urine, dark-black pigmentation of connective tissues (ochronosis), and arthritis of large joints and spine. The disease is usually diagnosed in adulthood by assessment of signs and symptoms of ochronosis. Confirmation of suspected diagnosis can be achieved by quantitative measurements of homogentisic acid levels. In this study, homogentisic acid was analyzed in 17 alkaptonuria patients. After liquid-liquid extraction, the analyte was determined by Gas Chromatography/ Mass Spectrometry (GC-MS) method. For quantitation purposes, external calibration was applied first, regression coefficient of ≥ 0.995 indicated the linearity in the concentration range of 1-100 ng/µl. The instrumental detection limit (IDL) and lower limit of quantitation were 3.82 and 12.7 µg/L, respectively. Recovery rate was ≥ 89%. Precision given as relative standard deviation (RSD) ranged from 3 -10 %. The results showed that the concentration of homogentisic acid ranged from 0.46 to 1.5 g/24 hours.