This study investigated, if genetic variants in BMP2, BMP4 and SMAD6 are associated with variations in the palatal rugae pattern in humans. Dental casts and genomic DNA from 75 patients were evaluated. Each patient was classified as follows: total amount of rugae; bilateral symmetry in the amount, length and shape of the palatal rugae; presence of secondary or fragmentary palatal rugae; presence of unifications; predominant shape; and predominant direction of the palatal rugae. The genetic variants in BMP2 (rs1005464 and rs235768), BMP4 (rs17563) and SMAD6 (rs2119261 and rs3934908) were genotyped. Genotype distribution was compared between palatal rugae patterns using the chi-square test (alpha = 0.05). The allele A was associated with the presence of secondary or fragmentary rugae for rs1005464 (OR = 2.5, 95%CI 1.1-6.3; p = 0.014). Secondary or fragmentary rugae were associated with the G allele in rs17563 (OR = 2.1, 95%CI 1.1-3.9; p = 0.017). rs17563 was also associated with rugae unification (p = 0.017 in the additive model). The predominant shape (wavy) was associated with rs2119261 (p = 0.023 in the additive model). The left-right symmetry of the length of primary rugae was associated with rs3934908 in the recessive model (OR = 3.6, 95%CI 1.2-11.7; p = 0.025). In conclusion, genetic variants in the BMP pathway impacted on palatal rugae pattern.