The rd3 retinal degeneration gene was previously mapped 10 +/- 2.5 cM distal to Akp1 on mouse Chromosome (Chr) 1 (Chang et al., 1993), a region that may be homologous to the locus of the human USH2A gene, which carries mutations responsible for Usher IIa retinal degeneration/hearing loss syndrome. An intercross from an Rb(11, 13)4Bnr(rd3/rd3) x C57BL/6J mating was set up, 428 F2 meioses were analyzed, and the rd3 gene was placed between the markers D1MIT292/D1MIT209 and D1MIT510, a distance of 1.40 +/- 0.57 cM. These flanking markers and the mouse ortholog of USH2A (Mush2a) were mapped in the T31 mouse radiation hybrid (RH) panel, with the result that D1MIT292/D1MIT209 and D1MIT510 were 7.9 cR3000 apart ( approximately 800 kb), and Mush2a was > 30 cR3000 proximal to the pair, excluding it from the rd3 locus. A contig spanning the rd3 locus and consisting of 2 YACs and one BAC was generated, and Mush2a was absent from it, confirming its exclusion from the locus. Comparison of adjacent marker pairs in the Whitehead genetic map and our genetic map showed some discrepancies in order of markers and genetic distances. Comparison of our genetic map and the RH map showed some highly skewed relationships between genetic and physical distances.