The present report describes the use of molecular probes to investigate the chromosomal constitution of interphase nuclei of formalin-fixed, paraffin-embedded tissue from three infants with multiple congenital malformations and a provisional diagnosis of trisomy 13 in two. Fluorescent in situ hybridization with the probe for the 13 and 21 centromeric regions revealed five nuclear signals in two of the cases, indicating the presence of an extra chromosome, and only four nuclear signals in the other case. Only the two positive cases had phenotypic features consistent with trisomy 13. Routine cytogenetic analysis was performed on one child and confirmed an additional chromosome 13. The child without an extra chromosome had features consistent with Ivemark syndrome. This study demonstrates the utility of fluorescent DNA probes for the retrospective diagnosis of aneuploidies in archival material.