The identification of subtelomeric rearrangements as a cause of mental retardation has made a considerable contribution to diagnosing patients with mental retardation. It is remarkable that for certain subtelomeric regions, deletions have hardly ever been reported so far. All the laboratories from the 'Association des Cytogénéticiens de Langue Française' were surveyed for cases where an abnormality of the subtelomere FISH analysis had been ascertained. Among 1511 cases referred owing to unexplained mental retardation, 115 (7.6%) patients showed a clinically significant subtelomeric abnormality. We report the clinical features and the molecular cytogenetic delineation of isolated de novo deletions on 20q13.33 in two cases. Detailed mapping was performed by micro-array CGH in one patient and confirmed by FISH in the two patients. We compare our data with the only three patients reported in the literature. Both patients shared a deleted region of approximately 1.33 Mb including 40 genes, with a 324 kb difference between the two patients. Haploinsufficiency for CHRNA4 and ARFGAP1 may have contributed towards a severe phenotype. In addition, the data in all patients suggest that haploinsufficiency for SOX18 may not cause the hypotrichosis-lymphedema-telangiectasia syndrome, or causes milder disease. Our study gives important information by defining the size of imbalance and better predicting the phenotype. Two clinically distinct phenotypes may be drawn, a mild mental retardation or a more complex and severe phenotype, according to the presence or absence of the CHRNA4 and ARFGAP1 genes respectively.