Orofacial clefts are common developmental disorders that pose significant clinical, economic and psychological problems. We conducted genome-wide association analyses for isolated cleft palate (CPO) and cleft lip with or without palate (CL/P) with ~17 million markers in sub- Saharan Africans. After replication and combined analyses, we identified novel loci for CPO at or near genome-wide significance on chromosomes 2 (near CTNNA2) and 19 (near SULT2A1). In situ hybridization of Sult2a1 in mice shows expression of SULT2A1 in mesenchymal cells in palate, palatal rugae and palatal epithelium in the fused palate. The previously-reported 8q24 locus was the most significant for CL/P in our study and we replicated several previously reported loci including PAX7 and VAX1.