In the present experiments, we studied the subcellular distribution of three types of extralysosomal, neutral proteolytic activities in rat telencephalon: (1) nonthiol proteases (NTP), (2) thiol proteases (TP), and (3) calcium-activated thiol proteases (calpains I and II). Subcellular fractionation was performed by using conventional differential and sucrose-gradient centrifugation techniques. The only significant proteolytic activity detected in crude homogenates could be assigned to calpain II, the high-threshold calcium-activated protease. Within the primary fractions prepared from the homogenates, the highest levels of calpain II were found in S3, or the soluble cytoplasmic fraction. Significant activity of the enzyme was also present in P2, the crude mitochondrial/synaptosomal fraction. In contrast, the specific activity of calpain I was greatest in P2 with somewhat lesser enzymatic activity in P1 and S3. Most of the calpain I in P2 was recovered after differential centrifugation through sucrose gradients and lysis of the resultant subfractions. In marked contrast, only a small percentage of the calpain II activity was recovered in the gradient bands. In all, calpain II appears to be predominantly localized in the soluble cytoplasmic compartment while the greatest concentrations of calpain I are found in the soluble components of small glial and neuronal processes (pinched off during homogenization) that constitute the P2 fraction. The highest specific activity of the calcium-independent proteases was obtained in P3, a fraction essentially devoid of calpain, with a secondary peak in P2. Subfractionation of P2 revealed that calcium-independent TP in P2 was associated with mitochondria while the calcium-independent NTP was more uniformly distributed across myelin, synaptosomes, and mitochondria.(ABSTRACT TRUNCATED AT 250 WORDS)