Genome-wide association studies (GWASs) and genome-wide linkage studies (GWLSs) have identified numerous risk genes affecting thesusceptibility to leprosy. However, most of the reported GWAS hits are noncoding variants and account for only part of the estimatedheritability for this disease. In order to identify additional risk genes and map the potentially functional variants within the GWAS loci,we performed a three-stage study combining whole-exome sequencing (WES; discovery stage), targeted next-generation sequencing(NGS; screening stage), and refined validation of risk missense variants in 1,433 individuals with leprosy and 1,625 healthy controlindividuals from Yunnan Province, Southwest China. We identified and validated a rare damaging variant, rs142179458 (c.1045G>A[p.Asp349Asn]) in HIF1A, as contributing to leprosy risk (p ¼ 4.95 3 10 ?9 , odds ratio [OR] ¼ 2.266). We were able to show that affectedindividuals harboring the risk allele presented with multibacillary leprosy at an earlier age (p ¼ 0.025). We also confirmed theassociation between missense variant rs3764147 (c.760A>G [p.Ile254Val]) in the GWAS hit LACC1 (formerly C13orf31) and leprosy(p ¼ 6.11 3 10 ?18 , OR ¼ 1.605). Byusingthe population attributablefraction,wehave shownthat HIF1Aand LACC1are themajorgeneswith missense variants contributing to leprosy risk in our study groups. Consistently, mRNA expression levels of both HIF1A and LACC1were upregulated in the skin lesions of individuals with leprosy and in Mycobacterium leprae-stimulated cells, indicating an active role ofHIF1A and LACC1 in leprosy pathogenesis.