A capillary electrophoresis method for determination of impurities in sodium cysteamine phosphate-an alternative drug to use in place of cysteamine (Cystagon), Mylan Laboratories Inc.) in the treatment of cystinosis-was developed. The administration of cysteamine, divided in four doses due to the short half-life of this drug, is a helpful treatment, but several patients show intolerance, due to the very unpleasant odor and taste of cysteamine. Sodium cysteamine phosphate is less organoleptic aversive and also has a larger active time, allowing the compression of the doses to 2 per day, increasing the acceptance of the drug. In the developed method the two main decomposition products of sodium cysteamine phosphate, cystamine and cysteamine, can be determined with LOQs of 30 microg/ml (0.2%) and 16 microg/ml (0.1%), respectively. The background electrolyte is 15 mM ammonium acetate (pH 8.85) with 10% methanol and the separation takes less than 4 min. UV detection is performed at 195 nm. This volatile method was developed with the purpose of further hyphenation to a mass spectrometer.