Fluorescent in situ hybridization (FISH) identified a cryptic balanced reciprocal translocation in the mother of an infant with the cri-duchat syndrome. A biotinylated probe from a flow-sorted chromosome 5 cosmid library was used to show the distal deletion of 5p15.2 in the propositus and a translocation of this segment to the distal end of 7 at 7p21 in his mother. In a subsequent pregnancy, the fetus was shown to have normal chromosomes using the same 5 cosmid library probe and a locus-specific probe derived from the 5p15.3 region. The importance of incorporating FISH into the routine diagnostic laboratory is discussed.