We have identified translocational intermediates generated during import of precursor proteins into the mitochondrial matrix and have characterized their association with mitochondrial membranes. Partially translocated forms of mitochondrial malate dehydrogenase (MDH) and ornithine transcarbamylase (OTC) were generated during import of the corresponding precursors (pMDH and pOTC) into mitochondria at 2°C. Import at this temperature results in the formation of intermediate-sized MDH (iMDH) and OTC (iOTC) produced by the removal of a portion of the leader peptide, and in the production of mature-sized MDH. All of these forms contain NH2 termini located within the mitochondrial matrix, although the majority of their polypeptide chains remain extramitochondrial. All three are strongly associated with mitochondrial membranes, but can be extracted by protein denaturants such as urea. These translocational intermediates appear to be hydrophilic proteins, on the basis of their partitioning properties during extraction with the nonionic detergent Triton X-114. The data indicate that the translocation of polypeptide chains into mitochondria occurs in a microenvironment that is aqueous in nature and is mediated by integral membrane proteins.