Blue native gel electrophoresis is a popular method for the determination of the oligomeric state of membrane proteins. Studies using this technique have reported that mitochondrial carriers are dimeric (composed of two ~32 kDa monomers) and, in some cases, can form physiologically relevant associations with other proteins. Here, we have scrutinised the behaviour of the yeast mitochondrial ADP/ATP carrier AAC3 in blue native gels. We find that the apparent mass of AAC3 varies in a detergent and lipid dependent manner (~60 to ~130 kDa) that is not related to changes in oligomeric state of the protein, but reflects differences in the associated detergent-lipid micelle and Coomassie dye used in this technique. Higher oligomeric state species are only observed under less favourable solubilisation conditions, consistent with aggregation of the protein. Calibration with an artificial covalent AAC3 dimer indicates that the mass observed for solubilised AAC3 and other mitochondrial carriers corresponds to a monomer. Size exclusion chromatography of purified AAC3 in decyl maltoside under blue native gel-like conditions shows that the mass of the monomer is ~120 kDa, but appears smaller on gels (~60 kDa) due to the unusually high amount of bound negatively charged dye, which increases the electrophoretic mobility of the protein-detergent-dye micelle complex. Our results show that bound lipid, detergent and Coomassie stain alter the behaviour of mitochondrial carriers on gels, which is likely to be true for other small membrane proteins where the associated lipid-detergent micelle is large compared to the mass of the protein.