The critical stage of palatal development is the fusion of apposing individual palatal shelves. Palatal shelves, from the day 13 murine embryo, cultured in vitro fuse normally in the absence of exogenous factors. Therefore, some endogenous factor(s) is responsible for the normal fusion process. Prevention of mature TGF-beta 3 activity during a specific time window of development in palate organ cultures, either by antisense oligodeoxynucleotides or neutralizing antibody, resulted in failure of palate fusion. Northern analysis was used to demonstrate that the antisense treatment down-regulated TGF-beta 3 mRNA. Inhibition of TGF-beta 1 or -beta 2 activity (by either antibodies or antisense oligodeoxynucleotides) had no such effect on palate development and palate fusion was normal. These data indicate an isoform specific role for TGF-beta 3 in palatal fusion.