A comparative pathology and mapping strategy was used to initiate a study on two bovine genetic diseases: arthrogryposis-palatoschisis and progressive ataxia, which affect mainly Charolais cattle. Bibliographic studies provided information on the pathology of these diseases, which helped to define similar diseases in other species. Animals affected by bovine arthrogryposis-palatoschisis display similar symptoms to those of muscular dysgenesis, mouse mutants and animals with progressive ataxia to those of Long Evans Shaker rat mutants. Candidate regions are respectively human chromosome 1q32 (BTA16) containing the gene CACNA1S and human chromosome 18q23 (BTA24) containing the gene myelin basic protein (MBP). Primer pairs were designed for 15 loci around each candidate gene, in a region of about 20 megabases and were used to screen a bovine Bacterial Artificial Chromosome (BAC) library. Eighteen microsatellites were found in the identified BAC clones, 11 on BTA24 and seven on BTA16. The genes and microsatellites were mapped by radiation hybrid (RH) analysis and a RH map was obtained for each region with 18 new localizations on BTA16 and 23 on BTA24. Comparative human-bovine analysis of the MBP region shows a good conservation of gene order while that of the CACNA1S region shows several breakpoints.