Hybrid isoelectric focusing of apolipoprotein A-I in polyacrylamide gels with immobilized pH-gradients under non-denaturing conditions resulted in the occurrence of additional bands which could prevent the specific and sensitive detection of genetic variants. Hybrid isoelectric focusing of two chromatographically distinguishable apolipoprotein A-I isoforms that differ by sulphoxidation of methionine residues, apo A-I(Met) and apo A-I(MetSO), revealed that the additional bands were caused by this post-translational modification. Several antioxidative additives and conditions were compared for their ability to prevent methionine sulphoxidation in apolipoprotein A-I. In the presence of 200 g/L mannitol in the gel, apolipoprotein A/I focused as a single band. Since methionine sulphoxidation in proteins is a general phenomenon either taking place in vivo or in vitro by isoelectric focusing, we conclude that isoelectric focusing in the presence of mannitol will improve the quality of resolution of many proteins in gels with immobilized pH-gradients.