OBJECTIVE: To investigate the association between bone morphogenetic protein 4 (BMP4) rs17563 polymorphism and nonsyndromic cleft lip with or without palate (NSCL/P) risk. METHODS: Four online databases were researched and the related publications were collected. Odds ratio (OR) with 95% confidence interval (CI) was applied to assess the relationship; publication bias, metaregression, and sensitivity analysis were conducted to guarantee the strength of results. RESULTS: Six published case-control studies were collected. Overall, no significant association between BMP4 rs17563 polymorphism and NSCL/P risk was found. It was notable that significant susceptibility on different ethnicity was observed in the stratified analysis. For Chinese population, the BMP4 rs17563 polymorphism was a significantly increased risk for NSCL/P (C versus T: OR = 1.52, 95% CI = 1.28-1.82, P < 0.01, I (2) = 0%; CC versus TT: OR = 2.58, 95% CI = 1.74-3.82, P < 0.01, I (2) = 0%; TC + CC versus TT: OR = 1.45, 95% CI = 1.14-1.84, P < 0.01, I (2) = 0%; CC versus TT + TC: OR=2.46, 95% CI = 1.46-4.14, P < 0.01, I(2) = 47.0%). On the contrary, significantly protective effects were found in Brazilian population (C versus T: OR = 0.69, 95% CI = 0.50-0.96, P = 0.03, I(2) = 68.5%; TC versus TT: OR = 0.52, 95% CI = 0.40-0.68, P < 0.01, I(2) = 0%; TC + CC versus TT: OR = 0.52, 95% CI = 0.35-0.78, P < 0.010, I(2) = 54.4%). CONCLUSION: This meta-analysis indicated that BMP4 rs17563 polymorphism could play a different role during the development of NSCL/P based on ethnicity diversity.