The aim of this prospective study is to determine the association of coffee and tea incidence as a factor for cleft lip and palate in Karnataka and Kerala population. This study took into account of mothers of 1000 non-syndromic oro-facial cleft subjects. They were questioned about their consumption of coffee –tea during first trimester and its frequency. Multiple logistic Regression for maternal coffee consumption during pregnancy shows that the odds ratio for mothers who consumed more than 3 cups was 1.84 ,1.31 and 1.23 with the confidence interval for the odds ratio was 1.46 to 1.99, 1.19 to 1.84, 1.06 to 1.45 in cleft lip, Cleft lip and palate and cleft palate group respectively. Whereas the odds ratio for tea is 1.65, 1.56, 1.33 with the confidence interval for the odds ratio being 1.28 to 1.93, 1.24 to 1.78 and 1.17 to 1.54 in CL, CLP, CP group respectively. Results from our study showed a dose dependent association between coffee and tea consumption during pregnancy and increased risk of oral cleft in their children.