Maternal phenylketonuria (mPKU) during pregnancy leads to the risk of spontaneous abortion or a teratogenic syndrome depending on the level of maternal phenylalaninemia. Mental retardation, microcephaly, congenital cardiopathy and intrauterine growth retardation are frequently seen in patients who intake an unrestricted diet before conception. The clinical picture shows variation in classic PKU. Severe neurological symptoms are not seen in all untreated cases of PKU syndromes. For this reason, mPKU can be seen in undiagnosed mothers. We hereby present a case who underwent investigations due to the presence of microcephaly and congenital cardiopathy. The diagnosis of PKU syndrome of the mother was determined following assessment of the baby. Furthermore, the unilateral renal agenesis that was detected in our case is the first case reported in the literature in which mPKU accompanies renal agenesis.