Fragile X syndrome (FXS) and Smith-Magenis syndrome (SMS) are associated with a number of specific topographies of problem behavior. Very few studies have examined the function served by problem behavior in these groups. Using the Questions About Behavioral Function scale Matson and Vollmer (User's guide: questions about behavioral function (QABF). Scientific Publishers Inc., Baton Rouge, LA, 1995) the current study examined group differences in the function of problem behavior displayed by children with FXS and SMS, in comparison to a control group of children with non-specific intellectual and developmental disabilities. Between-group analyses showed children with SMS were more likely to display problem behavior related to physical discomfort. Both within- and between-group analyses showed children with FXS were less likely to display attention-maintained problem behavior. These findings hold implications for the assessment, treatment and prevention of problem behavior associated with both FXS and SMS.