Keloid is a dermal fibroproliferative growth that results from dysfunction of the wound healing processes. Through a multistage genome-wide association study using 824 individuals with keloid (cases) and 3,205 unaffected controls in the Japanese population, we identified significant associations of keloid with four SNP loci in three chromosomal regions: 1q41, 3q22.3–23 and 15q21.3. The most significant association with keloid was observed at rs873549 (combined P = 5.89 × 10⁻²³, odds ratio (OR) = 1.77) on chromosome 1. Associations on chromosome 3 were observed at two separate linkage disequilibrium (LD) blocks: rs1511412 in the LD block including FOXL2 with P = 2.31 × 10⁻¹³ (OR = 1.87) and rs940187 in another LD block with P = 1.80 × 10⁻¹³ (OR = 1.98). Association of rs8032158 located in NEDD4 on chromosome 15 yielded P = 5.96 × 10⁻¹³ (OR = 1.51). Our findings provide new insights into the pathophysiology of keloid formation.