Our previous studies demonstrated that intravenous administration of staphylococcal enterotoxin B (SEB) to BALB/c mice resulted in thymocyte apoptosis. In the present study, we evaluated the role of protein kinase C (PKC) in thymocyte apoptosis induced by SEB. Our results showed that the level of protein phosphorylation in the thymocytes was reduced after the in vivo SEB treatment for 24 h. The activity of classical PKC subspecies was decreased in both cytosolic and membrane fractions of thymocytes following SEB administration. The lowest level of PKC activity was reached by 24 and 48 h, then was recovered gradually after 72 h. Furthermore, the mRNA expression of PKC-beta and, to a much less extent, PKC-alpha, but not PKC-sigma, in thymocytes was reduced by SEB. The decrease of mRNA level of PKC-beta showed good correlation with the pattern of PKC activity. These results provide direct evidence showing the changes in PKC subspecies mRNA expression during the process of apoptosis.