A phenotypically female infant with 46-XY chromosomes was found to have Smith-Lemli-Opitz syndrome, type II a rare congenital malformation syndrome with many features of the more common classic Smith-Lemli-Opitz syndrome. The patient's skeletal survey revealed characteristic and previously undescribed skeletal anomalies which are reported. In addition a lipoma of the pituitary gland was found on magnetic resonance imaging. This lesion is particularly interesting given the hypothesized steroid abnormality in Smith-Lemli-Opitz, type II syndrome, the sexual ambiguity of males with this syndrome and the similarity of this syndrome to the Pallister-Hall syndrome which characteristically has a hamartoblastoma of the hypothalamus.