Transfusion associated graft-versus-host disease (TA-GVHD) is a rare, dreadful complication of transfusion in immunocompromized and immunologically competent individuals. The diagnosis is often delayed, because of lack of awareness and the non-specific clinical features. We describe a rapid molecular cytogenetic analysis of FISH for the diagnosis of two cases of TA-GVHD with sex-mismatched donors. The use of FISH is a rapid and sensitive technique for the early diagnosis of TA-GVHD when the recipient and donor are of different gender.