AbstractCleft lip/palate comprises a large fraction of all human birth defects, and is notable for its significant lifelong morbidity and complex etiology. Several studies have shown that genetic factors appear to play a significant role in the etiology of cleft lip/palate. Human chromosomal region 9q21 has been suggested in previous reports to contain putative cleft loci. Moreover, a specific region (9q22.3–34.1) was suggested to present a ∼45% probability of harboring a cleft susceptibility gene. Fine mapping of 50 SNPs across the 9q22.3–34.11 region was performed to test for association with cleft lip/palate in families from United States, Spain, Turkey, Guatemala, and China. We performed family‐based analyses and found evidence of association of cleft lip/palate withSTOM(rs306796) in Guatemalan families (P = 0.004) and in all multiplex families pooled together (P = 0.002). This same SNP also showed borderline association in the US families (P = 0.04). Under a nominal value of 0.05, other SNPs also showed association with cleft lip/palate and cleft subgroups. SNPs inSTOMandPTCHgenes and nearbyFOXE1were further associated with cleft phenotypes in Guatemalan and Chinese families. Gene prioritization analysis revealedPTCHandSTOMranking among the top fourteen candidates for cleft lip/palate among 339 genes present in the region. Our results support the hypothesis that the 9q22.32–34.1 region harbors cleft susceptibility genes. Additional studies with other populations should focus on these loci to further investigate the participation of these genes in human clefting. © 2010 Wiley‐Liss, Inc.