We report on a Japanese boy with interstitial deletion of chromosome 12q12-q13.12, who had multiple congenital anomalies with severe psychomotor retardation. Most of the clinical manifestations were compatible with Noonan syndrome phenotype except for the absence of cardiac defects. Severe mental retardation and intrauterine onset of growth retardation may have been due to the chromosomal deletion. The interstitial deletion does not overlap a putative Noonan syndrome locus, which was recently assigned to 12q22-qter by linkage analysis. Although correlation between the phenotype and del(12)(q12q13.12) was not confirmed, because this is the first report of deletion of proximal 12q, the deleted segment may contain another Noonan syndrome locus.