A simple, automated colorimetric microassay system has been designed to quantitate enzyme activities commonly used as markers for subcellular compartments. This system relies on the spectrophotometric reading of microtiter wells containing the chromophore products. The microassay allows rapid, economical, and quantitative analysis of enzyme activities associated with sucrose or Percoll gradient fractions used for subcellular fractionation studies as well as the screening of a large number of fractions derived from HPLC and other separation columns used for enzyme purification. We describe its use for the quantitation of activities associated with acid and alkaline phosphatases, alkaline phosphodiesterase, beta-glucuronidase, alpha-N-acetylglucosaminidase, alpha-mannosidase, alpha-L-fucosidase, glycosidases, serine esterases, and succinate dehydrogenase, and give the range of their sensitivities. This microassay system has been applied to the isolation of granules of cytolytic lymphocytes and to the identification and purification of a serine esterase from the isolated granules of these cells.