The growing interest in combinatorial chemistry has led us to explore new analytical methods for the analysis of complex molecular libraries. Because an investigation of large mixtures with 10(4)-10(5) different chemical entities was not realistic, an alternative approach was pursued that included the analysis of small representative sublibraries using positive and negative ion electrospray mass spectrometry. The detailed analysis of these model mixtures, containing up to 55 components, allowed us to obtain important information about the composition of a library with considerable complexity. The results were used to improve the synthetic procedure in order to provide the maximum yield of expected library components. The applicability of mass spectrometry to the analysis of complex matrices and the usefulness of the technique for screening synthesized combinatorial libraries to probe their expected diversity and complexity have been demonstrated.