Analytical differential centrifugation of brown adipose tissue homogenates from cold-acclimated guinea pigs revealed a polydispersity of both mitochondria and peroxisomes, with at least two populations of each organelle. The estimated values were sH = 16685+/-4220 S and sL = 4792+/-951 S (mitochondria), and sH = 3364+/-1706 S and sL = 889+/-177 S (peroxisomes). Based on these s values, an optimal procedure is described for the isolation of subcellular fractions enriched in mitochondria and peroxisomes, respectively. 2. When the mitochondrial and peroxisomal fractions were subjected to isopycnic gradient centrifugation on a self-generating gradient of poly(vinylpyrrolidone)-coated colloidal silica particles (Percoll) in 0.25 M sucrose medium, buoyant densities of about 1.11 g/cm3 (main fraction of mitochondria) and 1.07 g/cm3 (main fraction of peroxisomes) were obtained. A value of 1.06 g/cm3 was found for the microsomal fraction. 3. The main peroxisomal fraction, isolated by gradient centrifugation, did not reveal any significant oxidation of palmitoyl-CoA as measured by conventional polarographic technique, whereas a small rate of oxidation (about 2.7+/-0.2 nmol/min per mg peroxisomal protein) was observed when measured as NAD+ reduction. This rate contributes no more than 1% of the mitochondrial oxidation of this fatty acid and it is, therefore, concluded that peroxisomal oxidation of the predominant long-chain fatty acids found in this tissue does not make a quantitatively significant contribution to fatty acid oxidation.