This investigation was carried out in the framework of a criminal case concerning substitution of a newborn infant. The subjects involved in the case were the child and its putative mother. Solution of the problem required typing two hypervariable mitochondrial DNA markers and 82 chromosomal markers. Moreover, we had to depart from the current norms according to which parentage can be excluded if two loci of the child contain alleles absent in the reputed parent. The present examination was complicated by the manifestation of a rare genomic mutation (unipaternal disomy) that necessitated extensive studies and taking non-trivial decisions. Details of this unusual case are highlighted and difficulties encountered in the course of investigation discussed to promote future analyses of chromosomal DNA mutations in parental gametes that hamper unambiguous interpretation of results of forensic examination.