The authors report the case of a Japanese girl with interstitial deletion of chromosome 12q15-q21.2 who had multiple congenital anomalies including bilateral cleft lip and palate (BCLP) with intrauterine onset of growth retardation and severe psychomotor developmental delay. Only two other patients with a similar deletion have been reported previously. However, these two patients showed such different clinical features that defining the karyotype-phenotype correlation has remained unfeasible. The additional case presented here reveals that two of the three cases with an overlapping deletion in 12q show the phenotype of BCLP, suggesting the correlation between this area of gene deletion and cleft lip and palate.