An automated method for analytical subcellular fractionation which utilizes routinely available reagents and equipment is described. Tissues are fractionated in Percoll density gradients and marker enzyme analysis of gradient fractions is performed with the Cobas-Bio centrifugal analyzer. Manual assays for cytochrome oxidase and protein were adapted for use with the instrument along with commercially available 5'-nucleotidase, lactate dehydrogenase, and acid phosphatase assay kits. Crude liver homogenate fractions containing different levels of enzyme activity were used to examine the linearity of the enzyme assays. The assays were shown to be linear at high and low levels of activity. Within-run precision studies using high and low activity liver homogenate pools were also performed, and a coefficient of variation of less than or equal to 5.5% was obtained for all assays. This method was used to analyze subcellular fractions from a Percoll density gradient separation of mouse liver homogenate material. The method allowed for a complete marker analysis, consisting of 96 separate kinetic assays, within 2 hours. The versatility of this method and the ease with which it can be performed should expand the use of analytical subcellular fractionation in the diagnostic laboratory.