Cleft lip and cleft palate occur when tissues in the baby's face and mouth don't fuse properly. Normally, the tissues that make up the lip and palate fuse together in the second and third months of pregnancy. But in babies with cleft lip and cleft palate, the fusion never takes place or occurs only part way, leaving an opening (cleft).
Researchers believe that most cases of cleft lip and cleft palate are caused by an interaction of genetic and environmental factors. In many babies, a definite cause isn't discovered.
The mother or the father can pass on genes that cause clefting, either alone or as part of a genetic syndrome that includes a cleft lip or cleft palate as one of its signs. In some cases, babies inherit a gene that makes them more likely to develop a cleft, and then an environmental trigger actually causes the cleft to occur.