Rs3762318 and rs2144658 were significantly associated with multibacillary leprosy. SNPs in high LD with rs3762318 and rs2144658 are eQTLs of SLC35D1. SLC35D1 mRNA expression was significantly decreased in leprosy skin tissues. Rare damaging missense variants in IL23R were enriched in leprosy patients. SLC35D1 and IL23R might be leprosy risk genes in Han Chinese.