With the description here of variant proteins A13 (pI 5.9, MW 62 kd) and A14 (pI 5.3, MW 26 kd), 14 polypeptides of mouse brain visualized by two-dimensional electrophoresis (2DE) exhibit genetic variation in isoelectric point. Using 22 B X D recombinant inbred strains, we map four of these loci and show that a fifth is independent of known loci. A pI 5.6, 81-kd protein of mouse brain mitochondria designated A1 is demonstrated to be an independent locus closely linked to LY-2 and LVP-1 on mouse chromosome 6. A pI 5.6, 28-kd genetically variant brain polypeptide designated A12 maps to chromosome 1 and shows identity with the known mouse locus LTW-4. The locus for A8 is not closely linked to any previously mapped locus. However, the locus for the newly described variant A13 shows 3 of 18 recombinants with the DNA polymorphism RN7S-2 and 2 of 18 recombinants with HC (hemolytic complement) and is thus probably located proximally to HC near the centromere of chromosome 2. Genetic and biochemical evidence is presented for the identification of A14 as ALP-1 (apolipoprotein 1), mapping to chromosome 9. In addition to these 13 genetically variant polypeptides, the positions of 12 other polypeptides which have been identified on 2DE gels of mouse brain are given.