Congenital malformations occur in numerous pig breeding programs. Clinical symptoms, etiopathogenesis and candidate genes of the most critical congenital malformations in pigs were briefly overviewed in the study. Based on the recent literature, identifying and evaluating the genomic regions associated with defects, such as splay legs syndrome, hernias, cryptorchidism, atresia ani, kyphosis, intersexuality, and malignant melanoma, can enhance the selection response. As promising genes were published e.g. NREP, FBXO32, and HOMER1 for splay leg syndrome, SRC, OSM, COL family, and CGRP for hernias, GNRHR, GATA2, and RLF for cryptorchidism, and GLI2 for atresia ani. Potential candidate genes associated with defects were mainly detected in literature by the genome-wide association approach. Reviewing the studies and following the suggestions in some of papers it is indicated the necessity for molecular and more comprehensive evaluation in terms of the sample standardisation and accurate phenotyping of a broad spectrum of populations and breeds. Moreover, knowledge transmission among all livestock species and humans is recommended in literature to better understand malformation biology.