chordomas arise in the skull base and spine and usually occur in adults and are rare in the pediatric population cases of chordoma in pediatric age are often poorly differentiated showing cytologic atypia increased cellularity and mitosis and their aggressive behavior is associated with a high incidence of metastatic spread and a short patient survival recent studies have described loss of smarcb1 ini1 protein in poorly differentiated chordomas associated not with point mutations but with smarcb1 ini1 gene deletions instead in this study we considered immunohistochemistry and smarcb1 ini1 mutational status to examine smarcb1 status in a series of pediatric chordomas 7 classic and 1 poorly differentiated we performed immunohistochemical tests for ini1 brachyury s100 and cytokeratins and conducted a genetic analysis on the smarcb1 coding sequence nm 003073 using the sanger method and multiplex ligation dependent probe amplification to detect abnormal copy numbers of the gene locus all 8 cases were positive for brachyury whereas there was no nuclear smarcb1 ini1 expression in 4 of the 8 cases including the poorly differentiated chordoma genetic analysis identified a missense mutation in 2 cases and a nonsense mutation associated with loss of smarcb1 ini1 protein and features of poorly differentiated tumor in 1 these mutations were novel variants occurring in heterozygosity and they were judged to be pathogenic by 3 different bioinformatic tools in 7 of 8 cases we performed multiplex ligation dependent probe amplification and 3 cases showed deletions at the smarcb1 locus our results confirm the pathogenic involvement of smarcb1 ini1 in childhood chordoma we also describe 3 novel pathogenic mutations.