This case report illustrates the unexpected identification of intrafamilial sexual abuse of a young mother through genetic testing of her child. The child’s genome was found to have a relatively common chromosomal condition with congruent clinical manifestations, but the microarray also suggested a close biological relationship between the parents because of a high degree of homozygosity. This prompted a child protection investigation as the mother had been a minor at the time of conception, and intrafamilial sexual abuse was confirmed. Both the intended and unintended results of microarray should be considered with respect to the health and social context of the child and their biological parents. This becomes particularly important for young mothers and raises protection concerns when significant amounts of homozygosity (consanguinity) are detected.