Our study results indicate that in humans with a cleft lip, the MSX2 gene is significantly more active postnatally in cleft lip tissue than relatively healthy oral mucosa tissue, which might be a compensatory mechanism, possibly caused by a disrupted WNT signaling pathway within cleft-affected tissue, which is indicated by the changes in other evaluated factors in cleft tissue, like the RYK gene and RYK protein. Here, MSX2 is linked to cleft lip.