Membranes were isolated from highly purified peroxisomes, mitochondria, and rough and smooth microsomes of rat liver by the one-step Na2CO3 procedure described in the accompanying paper (1982, J. Cell Biol . 93 :97-102) . The polypeptide compositions of these membranes were determined by SDS PAGE and found to be greatly dissimilar . The peroxisomal membrane contains 12% of the peroxisomal protein and consists of three major polypeptides (21,700, 67,700 and 69,700 daltons) as well as some minor polypeptides . The major peroxisomal membrane proteins as well as most of the minor ones are absent from the endoplasmic reticulum (ER) . Conversely, most ER proteins are absent from peroxisomes.By electron microscopy, purified peroxisomal membranes are -6 .8 nm thick and have a typical trilaminar appearance . The phospholipid/protein ratio of peroxisomal membranes is -200 nmol/mg; the principal phospholipids are phosphatidyl choline and phosphatidyl ethanolamine, as in ER and mitochondrial membranes. In contrast to the mitochondria, peroxisomal membranes contain no cardiolipin . All the membranes investigated contain a polypeptide band with a molecular mass of 15,000 daltons. Whether this represents an exceptional common membrane protein or a coincidence is unknown. The implications of these results for the biogenesis of peroxisomes are discussed.Knowledge of the peroxisomal membrane's properties is essential to an understanding both of the organelle's functions and of its biogenesis . The membrane separates the peroxisomal contents from the cytosol and defines the peroxisomal interior as a distinct intracellular space. The permeability properties of the membrane determine to what extent the peroxisome functions as a separate biochemical compartment. Knowledge of how the membrane is formed is essential to an understanding of the biogenesis of the organelle as a whole. If the membrane is derived from some other intracellular membrane, for example the endoplasmic reticulum (ER) (as is widely assumed), then one might expect to see some similarity in composition between them . If, on the other hand, the peroxisomes exist as a separate intracellular compartment, as has recently been suggested (1), then the peroxisomal membrane needs to have no structural similarity to the ER . THE JOURNAL OF CELL BIOLOGY " VOLUME 93 APRIL 1982 103-110 ©The Rockefeller University Press -0021-9525/82/04/0103/08 $1 .00We have applied the newly-developed sodium carbonate procedure described in the accompanying paper (2) to isolate peroxisomal, mitochondrial, and ER membranes.' We have partially characterized these three membranes, and found that their polypeptide compositions are almost entirely different, but their phospholipid compositions are similar. Some of these results have appeared in abstract form (3, 4) .' Rat liver microsomes were subfractionated by isopycnic centrifugation in linear sucrose gradients according to Beaufay et al. (7). The fractions selected as the "rough microsomal fraction" have been shown by these authors to c...