Because mitochondria have two membranes, the problem of protein insertion into these membranes is also a problem of protein sorting. Here, we discuss possible mechanisms for insertion into the mitochondrial outer or inner membrane for those proteins that are imported unidirectionally into the organelle, via a stop-transfer (non-conservative) pathway. For polytopic proteins, sorting presumably pertains only to the first insertion event since this predetermines membrane selection for subsequent insertion of the rest of the molecule. Models are proposed in which selection of the outer membrane is determined by an OMM signal-anchor sequence, in which the translocation and membrane anchor signals either overlap or are in close juxtaposition, and selection of the inner membrane is by a combination of a matrix-targeting signal and a distal stop-transfer sequence. We have employed manipulations that allow a protein containing an OMM signal-anchor sequence to by-pass the outer membrane and efficiently insert into the inner membrane, raising the possibility that potential regulation of the outer membrane protein translocation machinery (e.g., if applied by cytosolic factors or receptors) might influence sorting. Our discussion focuses on proteins that are anchored in the membrane by hydrophobic helical segments. Integral proteins that lack such structures (e.g., porin and ISP42/MOM38) may intercalate into the bilayer by a different mechanism.