A highly purified preparation of phosphatase-activating kinase (Fa) from rabbit skeletal muscle phosphorylated ribosomal protein S6. The two activities copurified on DEAE-Sephadex, CM-Sephadex, and phosphocellulose chromatography and upon further chromatography on Sephacryl S-300 and FPLC Mono-S and Mono-Q columns. On the latter column, two separate peaks of Fa activity were observed when it was developed in Tris buffer as opposed to beta-glycerophosphate. S6 kinase activity was obtained only with the Fa which adhered to the resin. The Mr of the Fa and S6 activities was determined to be 83,200 by gel permeation on a Sephacryl S-300 column. The Fa preparation phosphorylated serine residues on S6; two tryptic phosphopeptides, A and C, were identified by two-dimensional phosphopeptide analysis. The enzyme also showed good activity toward initiation factor eIF-4B. Based on specificity toward ribosomal proteins and initiation factors, the Fa and a mitogen-stimulated S6 kinase purified from insulin-stimulated 3T3-L1 cells were similar. These results suggest that a form of Fa and an insulin-stimulated S6 kinase may be related or closely associated.