The contribution of molecular mutations to the progression of Langerhans' cell histiocytosis (LCH) is not well understood. This study analyzes fractional allelic loss (FAL) across a series of tumor suppressor genes (TSGs) comparing LCH of various clinical stages and LCH involving organs of various degrees of prognostic risk. Polymerase chain reaction (PCR) amplification, using fluorescent-labeled primers targeting 6 TSGs, was performed on extracted DNA. The PCR products were analyzed using a capillary electrophoresis genetic analyzer. Ratios of the peak heights in informative cases were compared between unaffected and lesional tissue to identify loss of heterozygosity (LOH). Fisher's exact testing was used to analyze the results. Fourteen children with single-system involvement (SS-LCH) and 10 with multisystem involvement (MS-LCH) were included. High-risk or special-site organ involvement was seen in 13 children and low-risk organ involvement in 10. The mean FAL in MS-LCH (62.7%) was statistically significantly higher than in SS-LCH (40.3%). The FAL in children with risk or special-site LCH (53.2%) was also significantly higher than in children with low-risk LCH (39.6%). Markers on 5q had significantly higher FAL in MS-LCH (76.3%) and children with risk or special-site organ involvement (72.7%) compared with SS-LCH (46.2%) and children with low-risk organ involvement (37.5%). These data suggest that more extensive and higher-risk forms of LCH have evidence of more mutational events at TSGs. Further investigation of the potential use of LOH at 5q23 will be necessary to establish utility for this assay to predict disease progression and poor outcome.