The first quantitative trait locus (QTL) in pigs, FAT1, was found on chromosome 4 using a wild-boar intercross. Further mapping has refined the FAT1 QTL to a region conserved on both human chromosome 1 and 8. We have now improved the comparative map of the entire SSC4 by mapping 105 loci to pig chromosome 4 (SSC4) and defined the specific human chromosome region with conservation to FAT1, using a combination of physical and linkage mapping. These types of analysis have resulted in maps with very good agreement. Comparative analysis revealed that the gene order is very well conserved across SSC4 compared to both human chromosome 1 (HSA1) and to HSA8. This refined SSC4 map and the comparative analysis will be a great aid in the search for the candidate genes for the FAT1 locus.