Parental imprisonment has been linked to a variety of adverse psychological outcomes for children and adolescents. The Strengths and Difficulties Questionnaire (SDQ) has been widely used to assess behavioural and emotional difficulties among 7–17 year olds in the general population and more recently has been utilised among samples of children of prisoners. Previous research has variously tested traditional one-, three- and five- factor solutions to the SDQ, and more recently one bifactor solution has been examined. Based on a sample of children of prisoners (N = 724) and their non-imprisoned parent or caregiver (N = 658), the aim of the present study was to simultaneously compare nine alternative factor structures, including previously tested models and alternative bifactor solutions. Tests of factorial invariance and composite reliability were also performed. The five-factor model was found to provide the best fit for the data. Tests of factorial invariance revealed that the five-factor model provided an equally acceptable, but not identical fit, among boys and girls. Composite reliability scores were low for the Conduct Problems and Peer Problems subscales. The utility of the SDQ in measuring psychological functioning in response to parental imprisonment is discussed.