We report a congenital anomalous fetus with holoprosencephaly, prenatally diagnosed by sonography and MR scan at the twenty-sixth week during the gestational period. Chromosome analysis by amniocentesis revealed trisomy 13 (47,XY,+13). The diagnosis was confirmed by autopsy. After induction, external examination showed a proboscis-like nose on the normal nose position. The right foot showed polydactylia with wide separation of the fifth and sixth toes. We found that the mother was an abuser of amphetamine at an early gestational age. The teratogenic effect of D-amphetamine on animals has been noted, but no previous clinical case of a congenital anomalous fetus and maternal abuse of amphetamine has been reported. This case report is the first to reveal holoprosencephaly and trisomy 13, with maternal early gestational abuse of amphetamine.