The formation and development of the secondary palate occurs through signalling molecules SHH, BMP-2, FGF-8, among others.

The elevation of the palatal shelves from a vertical position to a horizontal one occurs during week 8 of embryological development.

The direct cause of this movement is unknown, but a number of possibilities have been identified as follows: Fusion between the two palatal shelves occurs during week 9 of embryonic development.

In this time, the elevated palatal shelves join together to form one continuous structure, with the medial edge epithelium (the shelf surfaces which are closest to each other) disappearing.

The specific mechanism by which the medial edge epithelium disappears has been differed over by academics.