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The importance of maternal smoking in the pathogenesis of oral facial clefts is not clear. Susceptibility to cigarette smoke depends on biotransformation of the toxic compounds by mother and embryo. In a population-based case-control study, we investigated the effects of maternal smoking during the first pregnancy trimester and the interaction with polymorphisms in the biotransformation enzymes cytochrome P450 1A1 (CYP1A1) and glutathione S-transferase theta 1–1 (GSTT1) on the risk of nonsyndromic oral clefting in the offspring. We recruited 113 infants with nonsyndromic oral clefts and their mothers, as well as 104 control infants and their mothers. Maternal smoking habits were collected regarding the period 3 months before through 3 months after conception. Buccal swabs were taken from mothers and infants for genetic analysis. Maternal smoking was not strongly associated with oral clefting (odds ratio = 1.1; 95% confidence interval = 0.6–2.2), nor were CYP1A1 and GSTT1 polymorphisms. Mothers who smoked and carried the GSTT1-null genotype, however, had an increased risk for having a child with oral clefting compared with nonsmokers with the wild type genotype (odds ratio = 3.2; 95% confidence interval = 0.9–11.6). The risk was almost five times greater (odds ratio = 4.9; 95% confidence interval = 0.7–36.9) in mothers and infants both having the GSTT1-null genotype compared with both having the wild genotype. There was no interaction between CYP1A1 and maternal smoking in relation to oral clefting.