Treacher Collins syndrome is an autosomal dominant, craniofacial developmental disorder, and its locus (TCOF1) has been mapped to chromosome 5q3. To refine the location of the gene within this region, linkage analysis was performed among the TCOF1 locus and 12 loci (IL9, FGFA, GRL, D5S207, D5S210, D5S376, CSF1R, SPARC, D5S119, D5S209, D5S527, FGFR4) in 13 Treacher Collins syndrome families. The highest maximum lod score was obtained between loci TCOF1 and D5S210 (Z = 10.52; theta = 0.02 +/- 0.07). The best order, IL9-GRL-D5S207/D5S210-CSF1R-SPARC-++ +D5S119, and genetic distances among these loci were determined in the 40 CEPH families by multipoint linkage analysis. YAC clones were used to establish the order of loci, centromere-5'GRL3'-D5S207-D5S210-D5S376-CSF1R -SPARC-D5S119-telomere. By combining known physical mapping data with ours, the order of chromosome 5q3 markers is centromere-IL9-FGFA-5'GRL3'-D5S207-D5S210- D5S376-CSF1R-SPARC-D5S119-D5S209- FGFR4-telomere. Based on this order, haplotype analysis suggests that the TCOF1 locus resides distal of CSF1R and proximal to SPARC within a region less than 1 Mb in size.