Germ-line and acquired mutations of the hSNF5/INI1 tumor suppressor gene have been reported in central nervous system (CNS), renal, and soft-tissue rhabdoid tumors. The present study was designed to compare the types of INI1 alterations among tumors from diverse anatomical sites and identify mutation hot spots. Fluorescence in situ hybridization and PCR-based microsatellite, heteroduplex, and sequence analysis were used to characterize chromosome 22 deletions and INI1 mutations among 100 primary rhabdoid tumors. Deletions and/or mutations of INI1 were detected in 75 patients, including 42 children with atypical teratoid/rhabdoid tumors of the brain or spinal cord and 6 children with a brain and a renal or soft-tissue tumor. Nineteen tumors arose in the kidney (in one child, bilaterally) and eight tumors were extra-renal. Homozygous deletions detected by fluorescence in situ hybridization were most often seen in CNS and extra-renal rhabdoid tumors, whereas truncating mutations were detected in a high percentage of CNS and kidney tumors. The highest frequencies of INI1 mutations for kidney tumors were seen in exons 2, 6, and 7, compared with exons 5 and 9 for CNS tumors. Two potential hot-spot mutations for CNS atypical teratoid/rhabdoid tumors were noted, including a C-to-T transition in codon 201 in exon 5 and a cytosine deletion in exon 9. Germ-line mutations were noted in 10 children, including 4 patients with two primary tumors. The majority of rhabdoid tumors from all sites contained deletions and/or mutations of the INI1 gene. Specific mutations were nonrandomly associated with anatomical site.