The biogenic amines, putrescine, cadaverine, spermidine and spermine were separated and quantified by capillary electrophoresis with pulsed amperometric detection. Detection potential of the pulsed amperometric detection was optimized as 0.6 V. Optimal separation of the biogenic amines was achieved using a separation buffer of 30 mM citrate at pH 3.5, while keeping the buffer in the detection cell as 20 mM NaOH. Using these conditions, the four biogenic amines were baseline separated. Extrapolated limits of detection for putrescine, cadaverine, spermidine and spermine were 400, 200, 100 and 400 nM for the standard mixture (polyamines dissolved in running buffer), respectively. These are lower than ultraviolet detection and comparable or even lower than laser-induced fluorescence detection results as reported in the literature. The number of theoretical plates was maintained at the 10(5) level, which is absolutely higher than any reported method. When applying capillary electrophoresis-pulsed amperometric detection to milk analysis, only spermidine was found in amounts varying between 0.1 and 0.5 mg/kg.