A family of structurally related carrier proteins mediates the flux of metabolites across the mitochondrial inner membrane. Differently from most other mitochondrial proteins, members of the carrier family are synthesized without an amino-terminal targeting sequence. However, in some mammalian and plant species, representatives were identified that carry a positively charged presequence. To obtain data on a carrier protein from lower vertebrates, we determined the primary structure of eel mitochondrial citrate carrier (CIC) and investigated its import pathway into the target organelle. The protein carries a cleavable presequence of 20 amino acids, including two positively charged residues. The cleavage site is recognized by a magnesium-dependent peptidase in the intermembrane space. The presequence is dispensable both for targeting and translocation, but prior to import into mitochondria, significantly increases the solubility of the precursor protein. This effect is completely retained if the positive charges are exchanged with negative charges. Following this observation, we found that several carrier proteins appear to carry non-cleavable presequences that may similarly act as charged intramolecular chaperones.