AbstractBACKGROUND:AXIN2andCDH1genes play important roles during craniofacial morphogenesis. Mutations in these genes have been described in families presenting colorectal cancer and tooth agenesis, and gastric cancer and cleft lip/palate (CL/P). Oral clefts have been associated with tooth agenesis. We investigated ifAXIN2andCDH1polymorphisms were associated with clefts or with any associated dental subphenotypes.METHODS:Markers inAXIN2andCDH1were genotyped using Taqman chemistry in a sample cohort comprised of 500 cleft individuals and 500 unrelated controls.RESULTS:Comparison between cleft and control groups showed a trend for association forAXIN2with incomplete cleft palate (p= .006) andCDH1with unilateral CL/P (p= .03 for left CL/P andp= .04 for right CL/P). Comparison of cleft subphenotypes with tooth agenesis and controls revealed borderline associations forCDH1(p= .008) andAXIN2(p= .01) with unilateral right CL/P with tooth agenesis.CONCLUSIONS:We observed only borderline results for the association ofAXIN2andCDH1with CL/P with and without tooth agenesis. Nevertheless, implication of these genes in the simultaneous occurrence of CL/P and cancer, and in tooth agenesis and cancer, is rather intriguing and warrants further investigations with other geographic and ethnic populations. Birth Defects Research (Part A), 2009. © 2008 Wiley‐Liss, Inc.