Twelve polymorphic markers identified by restriction fragment length polymorphism (RFLP) analysis or simple sequence repeat (SSR) polymorphism analysis were assigned to rat chromosome 1 by linkage analysis of F2 intercross progeny of F344/N and LEW/N inbred rat strains. One linkage group, covering 46.3 cM, consisted of eight markers including five genes, TNT (fast skeletal troponin T), IGF2 (insulin-like growth factor 2), MYL2 (MLC2 gene for muscle myosin light chain 2), ALDOA (aldolase A), and HBB (hemoglobin beta-chain); one anonymous locus, D1N64; one marker related to the carboxypeptidase B gene, CARB07-related sequence; and one marker related to the parathyroid hormone gene, PTH-related sequence. A second linkage group, covering 45.0 cM, consisted of three markers including two anonymous loci, 2B1 and D1N40, and one gene, TCP1 (T-complex 1). INS1 (insulin 1), which has been previously assigned to rat chromosome 1, was not linked to these markers. The SSR markers were highly polymorphic in 13 inbred rat strains (SHR/N, WKY/N, MNR/N, MR/N, LOU/MN, BN/SsN, BUF/N, WBB1/N, WBB2/N, ACl/N, LER/N, F344/N, and LEW/N). These markers, located on chromosome 1, will be useful in genetic studies in rats.