Background: The phenotype of children and adults with fragile X syndrome (FXS) includes a number of problem behaviours such as inattention, social anxiety and aggressive outbursts. However, very little work has been conducted with young children with FXS less than 5 years of age to examine the developmental pathway of problem behaviours in this population and to determine if later occurring problem behaviours may be rooted in early appearing temperament profiles. Methods: Parent ratings and laboratory-based behavioural observations of negative reactivity were examined in 25 3-year-old boys with FXS and compared with 64 typically developing boys matched on age. Results: Compared with the typically developing group, boys with FXS were rated by their parents as exhibiting less anger and sadness on the "Child Behaviour Questionnaire" (CBQ), and they showed less facial sadness on the Laboratory Temperament Assessment Battery (Lab-TAB). No group differences were found on the Lab-TAB measures of distress vocalisations, bodily struggle, and facial anger; and anger peaked in the middle of the arm restraint episode for both groups. For boys with FXS, mental age was moderately positively correlated, and autistic behaviour was moderately negatively correlated, with sadness scores from the CBQ. Conclusions: Our results show different behavioural profiles in very young children with FXS than reported in older-aged children with FXS which implies that temperamental differences and elevated problem behaviours reported in older-aged children with FXS may not be rooted in early temperament. This information is important to develop the phenotype of early development in FXS to facilitate early identification and treatment.