Trisomy 9p syndrome was first described by Rethore et al in 1970 and about 150 cases have been reported. The characteristic features of the partial trisomy 9p syndrome is clearly recognizable faces, which include microcephaly, facial deformities, skeletal and dermatoglyphic anomalies with variable degrees of mental retardation. The 3-ketothiolase deficiency was first described in 1971 and about 30 cases have been reported. The 3-ketothiolase deficeiency is an inborn error of isoleucine and ketone body catabolism that shows autosomal recessive traits, caused by a deficiency of mitochondrial acetoacetyl-coenzyme A thiolase(T2). We report a case of partial trisomy 9p syndrome with 3-ketothiolase deficeiency in a 4-years-old female. The karyotype of the patient was confirmed as 46,XY, add(9)(p23) mat. In the urine organic acid test, 3-ketothiolase deficiency was reported.