Hemophagocytic syndrome (HS) is a histiocytic reactive process often associated with infections and/or malignancies. Clonal karyotypic abnormalities have been the hallmark of several hematological malignancies and have been shown to be of clinical significance in terms of both diagnosis and prognosis. While there are limited reports of both clonal and nonclonal abnormalities in HS, their clinical significance has not been established. Detection of such clonal abnormalities, as seen in some cases of HS, may indicate the presence of an occult malignant process, even when there is no microscopic evidence of a hematological malignancy. We report a case of HS in a child with clonal t(4;7)(q21;q36) which later progressed to acute myeloid leukemia (AML) with further clonal evolution. Our case strengthens the argument that cytogenetic studies in HS may be important in identifying the underlying occult malignant process.