Nonsyndromic cleft lip with or without cleft palate is a common birth defect with a wide range of prevalence among different populations, apparently highest in Asians and Amerindians and lowest in Africans. Recent genomewide association studies of European-derived and Asian populations have identified six confirmed loci for this phenotype: 1p22.1, 1q32.2 (IRF6), 8q24, 10q25.3, 17q22, and 20q12. However, there have thus far been no studies of these loci in African patients with nonsyndromic cleft lip with or without cleft palate. We carried out association analysis of SNPs in these six candidate chromosomal regions in 128 nonsyndromic cleft lip with or without cleft palate cases and 105 controls from the Rift Valley of Kenya. We observed no apparent association of this phenotype with any of these SNPs, though there was strong statistical power only for 8q24. These results indicate that at least the 8q24 locus does not play a major role in the pathogenesis of nonsyndromic cleft lip with or without cleft palate in east Africa, supporting locus heterogeneity for susceptibility to this phenotype among different major populations of the world. © 2011 Wiley-Liss, Inc.