We previously reported that mutation of the transforming growth factor-β3 (TGF-β3) gene caused cleft palate in homozygous null (−/−) mice. TGF-β3 is normally expressed in the medial edge epithelial (MEE) cells of the palatal shelf. In the present study, we investigated the mechanisms by which TGF-β3 deletions caused cleft palate in 129 × CF-1 mice. For organ culture, palatal shelves were dissected from embryonic day 13.5 (E13.5) mouse embryos. Palatal shelves were placed singly or in pairs on Millipore filters and cultured in DMEM/F12 medium. Shelves were placed in homologous (+/+ vs +/+, −/− vs −/−, +/− vs +/−) or heterologous (+/+ vs −/−, +/− vs −/−, +/+ vs +/−) paired combinations and examined by macroscopy and histology. Pairs of −/− and −/− shelves failed to fuse over 72 hours of culture whereas pairs of +/+ (wild-type) and +/+ or +/− (heterozygote) and +/−, as well as +/+ and −/− shelves, fused within the first 48 hour period. Histological examination of the fused +/+ and +/+ shelves showed complete disappearance of the midline epithelial seam whereas −/− and +/+ shelves still had some seam remnants. In order to investigate the ability of TGF-β family members to rescue the fusion between −/− and −/− palatal shelves in vitro, either recombinant human (rh) TGF-β1, porcine (p) TGF-β2, rh TGF-β3, rh activin, or p inhibin was added to the medium in different concentrations at specific times and for various periods during the culture. In untreated organ culture −/− palate pairs completely failed to fuse, treatment with TGF-β3 induced complete palatal fusion, TGF-β1 or TGF-β2 near normal fusion, but activin and inhibin had no effect. We investigated ultrastructural features of the surface of the MEE cells using SEM to compare TGF-β3-null embryos (E 12.5-E 16.5) with +/+ and +/− embryos in vivo and in vitro. Up to E13.5 and after E15.5, structures resembling short rods were observed in both +/+ and −/− embryos. Just before fusion, at E14.5, a lot of filopodia-like structures appeared on the surface of the MEE cells in +/+ embryos, however, none were observed in −/− embryos, either in vivo or in vitro. With TEM these filopodia are coated with material resembling proteoglycan. Interestingly, addition of TGF-β3 to the culture medium which caused fusion between the −/− palatal shelves also induced the appearance of these filopodia on their MEE surfaces. TGF-β1 and TGF-β2 also induced filopodia on the −/− MEE but to a lesser extent than TGF-β3 and additionally induced lamellipodia on their cell surfaces. These results suggest that TGF-β3 may regulate palatal fusion by inducing filopodia on the outer cell membrane of the palatal medial edge epithelia prior to shelf contact. Exogenous recombinant TGF-β3 can rescue fusion in −/− palatal shelves by inducing such filopodia, illustrating that the effects of TGF-β3 are transduced by cell surface receptors which raises interesting potential therapeutic strategies to prevent and treat embryonic cleft palate.