In a linkage analysis of Pax-3 and splotch no recombinations were found in 117 backcross mice. Molecular analysis of Pax-3 in three alleles of splotch shows a number of significant alterations to the Pax-3 gene. In Sp/Sp embryos, cDNA PCR analysis reveals a shortened transcript in which exon 4 of Pax-3 is deleted due to mutation of the splice acceptor site of intron 3. In the Sp4H allele, the Pax-3 gene is deleted and in Spd embryos, Pax-3 expression is significantly lower than that in normal littermate embryos. The linkage analysis, shortened Pax-3 transcript in Sp, and deletion of Pax-3 in Sp4H described here, together with the previous report of an intragenic deletion in Pax-3 in Sp2H mice and the deletion of Pax-3 in Spr mice, provide strong evidence for the allelic identity of Pax-3 and Sp.