The investigation of mitochondrial abnormalities in brain commonly requires isolation of these organelles from small tissue samples. We have modified a mitochondrial isolation procedure based on Percoll density gradient centrifugation to increase the proportion of the total mitochondrial pool recovered while reducing contamination with synaptosomes and related structures containing cytoplasm. Initially, myelin was removed by centrifugation in 12% Percoll in isotonic buffer. The pellet was resuspended, treated with digitonin to break up synaptosomes and similar structures and subjected to discontinuous Percoll density gradient centrifugation. The mitochondrial fraction obtained from this procedure was highly metabolically active and well coupled, exhibiting respiratory control ratios above 5. The recovery of mitochondrial markers using a single rat forebrain as starting material was approximately 18% to 21%. When small tissue samples (approximately 50 mg wet weight) were used as starting material the recovery of the mitochondrial marker was approximately 16%. The ratio of recovery of a mitochondrial marker to the cytoplasmic marker lactate dehydrogenase exceeded 200 in preparations from a single rat forebrain. This is substantially greater than values reported for previously published procedures reflecting both an improved yield of mitochondria and a reduction in cytoplasmic contamination.