We report here our experience in the management of four children undergoing sex mismatched allogeneic bone marrow transplantation (BMT) who showed evidence of poor engraftment post BMT. Fluorescence in situ hybridisation (FISH) was performed on direct bone marrow smears with the X centromere and Y heterochromatin probes, to ascertain chimerism. Of 16 hybridisations, only one was unsuccessful, whereas routine bone marrow cytogenetics performed at the same time failed in five of eight cultures. The FISH results were available in one to two days. The FISH findings provided a valuable aid in the early management of these children.