The potential utility of capillary electrophoresis CE as an analysis and biological assay method for rapid screening of single-component combinatory libraries is demonstrated by mimicking a 5 = 5 drug matrix. Twenty-five com-ลฝ . pounds some drugs, vitamins, metabolites, etc. that include biotin are selected as the test analytes and avidin is treated as the biological activity screening reagent. In order to rapidly screen the compounds, five mixtures of nine components each are created at the diagonal of the matrix by pooling each component from the same column and row. The separation power of CE and related techniques is such that the components in these randomly generated nine-compound mixtures are almost always resolved using a single logical set of separation conditions. After obtaining optimum separation conditions, affinity testing produces the locations of ลฝ . the possible active component s based on changes in peak area. Blind tests are ลฝ . conducted that successfully locate the active component s of the matrix. With each ลฝ . test requiring about 14 separations 7 with and 7 without avidin and each separation within 15 min, we were able to analyze the mixture and identify the ลฝ exact locations of two possible active compounds biotin and an unexpected . compound in the 5 = 5 matrix. The effect of avidin concentration on the screening procedure is assessed. Another protein, myglobin, was tested to compare specific ลฝ and nonspecific interactions and to assign a threshold value percent decrease in . peak area for determining a positive affinity response.