Qualitative aspects of protein synthesis in organelles and intact cultured cells of brain origin were compared to clarify the distinction between synaptosomal and mitochondrial protein synthesis. Brain mitochondria and synaptosomes were isolated either on a traditional Ficoll-sucrose gradient or by a new Percoll gradient procedure, and were incubated in an amino acid incorporation system containing [35S]methionine, then electrophoresed on gradient slab gels. Autoradiography of the gels revealed that in the presence of cycloheximide both mitochondria and synaptosomes synthesized at least 17 proteins in the 6,000-50,000 MW range, and that incubation with chloramphenicol reduced or eliminated these bands. With minor variation these patterns in the low-molecular-weight region also resembled patterns obtained from cycloheximide-inhibited rat liver mitochondria and intact brain cells (cultured glia, glioma, and neuroblastoma). In the higher molecular weight region of the gels (greater than 50,000) banding patterns were more complex and tended to differ between organelles and intact cells. These polypeptides probably reflect nonmitochondrial protein synthesis, and their variable response to inhibitors may account for confusion in the literature with regard to the effects of inhibitors of protein synthesis in brain mitochondria and synaptosomes.