In this paper, we present a comparative analysis of hierarchical clustering and multidimensional scaling methods for genotype and phenotype data analysis. Fisher's exact test was applied to determinate dependencies between congenital anomalies. In order to determine the relationship between the dependences of congenital anomalies, deformations, these systems’ micro anomalies and congenital anomalies associated with orofacial clefs, the Spearman and Kendall correlation coefficients were applied. It has been detected which methods are better for genetic data visualization.