We previously demonstrated that the translocation of phospholipids between the mitochondrion and the endoplasmic reticulum occurs via highly specialized membrane microdomains of both organelles that are in situ closely associated. As understanding of the interactions between both organelles requires characterization of the translocation sites organization, we first analysed the amino acid compositions of these sites. Using principal component analysis, we have shown that the translocation sites exhibit characteristic patterns when compared with the membranes from which they are derived. The results are discussed in terms of both functional and structural microcompartmentation within the membranes of mitochondria and endoplasmic reticulum.