A capillary electrophoresis method with diode array detection for quantitative analysis of histamine (HIS) in cheese was developed and validated. The electrophoretic conditions studied for method optimization were buffer concentration (25-100 mM) and pH (2.5-6.5), voltage (10-30 kV) and temperature (20-35°C). The effects of these conditions on peak shape, sensitivity and migration time were tested. The optimized method was validated for linearity, sensitivity, accuracy, precision (intraday and interday repeatability) and recovery. The limit of detection (LOD) and limit of quantitation (LOQ) values of the validated method were determined as 20 mg/kg and 61 mg/kg for HIS, respectively. This method was successfully applied for quantitative analysis of HIS in 16 traditional cheese samples obtained from different Turkish markets. Histamine was detected in 15 samples (94%) with a level greater than LOD, and in 2 (13%) samples greater than LOQ, with the values of 91.5 and 65.9 mg/kg.