A method based on the use of capillary zone electrophoresis (CZE) is proposed for the determination of the heterologous protein bovine pancreatic trypsin inhibitor (BPTI) expressed in yeast. Saccharomyces cerevisiae cells were transformed with plasmid pCB235U and the amount of inhibitor expressed in yeast was measured both in the culture medium (supernatant) and the cell extract. Supernatant samples were investigated by the CZE method preceded by affinity chromatography (the BPTI yield was between 2 and 5 μg ml−1); direct determination of BPTI in cell extract was performed taking advantage of the complex formation of BPTI and trypsin (BPTI yield was 5 μg ml−1).