The aim of this study was to evaluate the influence of the γ-aminobutyric acid receptor type A β-3 subunit (GABRB3) polymorphisms in patients with nonsyndromic cleft lip and/or palate (NSCL/P). We carried out a structured case-control analysis of three GABRB3 polymorphisms (rs4477673, rs6576618, and rs981778) in 229 patients with nonsyndromic cleft lip with or without cleft palate (CL±P) and in 314 unaffected controls from Brazil. The polymorphisms were genotyped by the TaqMan 5'-exonuclease allelic discrimination assay, and each sample was independently typed for 40 biallelic short insertion/deletion markers (INDELs) to characterize the genomic ancestry. The genotype distributions of the three polymorphisms were as expected by the Hardy-Weinberg equilibrium test. After adjustment to ancestry contribution, the minor A allele of rs981778 was associated with NSCL/P, but significant results did not persist after Bonferroni correction for multiple tests. Similarly, the haplotype analysis revealed that the CCA haplotype (C allele of rs4477673, C allele of rs6576618, and A allele of rs981778) was correlated with NSCL/P, but this association did not remain statistically significant after Bonferroni correction. With a weak association, our data do not support the hypothesis that the GABRB3 variants are a cause of NSCL/P, but further studies are warranted.