A capillary electrophoresis (CE) method has been developed and optimized for the detection of Gly-Pro dipeptide in complex biological samples: medium, cell layer and matrix obtained from long term cultured human fibroblasts of control and prolidase deficiency patients. The influence of different detergents in the sample preparation and electrophoretic conditions were investigated. The method was validated for cellular extracts with respect to limits of detection and quantitation, precision, linearity, accuracy and robustness. The optimized method was applied to real samples and revealed a significant increase of intracellular Gly-Pro dipeptide in prolidase deficiency fibroblasts with respect to the control.