Two sisters presented with multiple congenital abnormalities and developmental delay; abnormalities elsewhere in their extended family suggested that their father carried a balanced translocation. G-banded chromosome analysis showed apparently normal karyotypes. Fluorescence in situ hybridisation (FISH) with whole chromosome paints revealed no apparent abnormality in the father. However, further FISH studies, using multiple subtelomeric probes, demonstrated a derivative chromosome 16 in one sister. Subsequent studies showed that her sister also had a derivative 16 which had been inherited in an unbalanced form from their father, who carried a balanced reciprocal translocation between chromosomes 1 and 16. This report describes the detection of this submicroscopic translocation and the clinical findings in the two sisters.