Cytogenetic and molecular studies have shown that approximately 80% of cases of alveolar rhabdomyosarcoma (ARMS) have consistent chromosomal translocation of either t(2;13) or t(1;13), resulting in either PAX3-FKHR or PAX7-FKHR gene fusions. However, 20% of the cases diagnosed histologically are negative for these fusion genes. The clinical and pathological properties of the so-called fusion gene negative tumors remain to be defined. We present an unusual case of a 7-year-old boy who developed three separate primary ARMS over a 5-year period, with the first tumor diagnosed at the age of 12 months. The tumors were negative for the characteristic translocations, t(2;13) or t(1;13), but showed evidence of low-level chromosomal instability and a reciprocal chromosomal translocation t(6;11)(q27;q13). PCR amplification of the p53 gene, exons 2-11, followed by DNA sequencing did not detect any germline p53 mutation. These clinical and cytogenetic features have not been reported previously in ARMS. The findings suggest that cytogenetic abnormalities of chromosome 6 may be associated with the development of early onset multiple ARMS in a subgroup of pediatric patients as seen in this case.