The Strengths and Difficulties Questionnaire (SDQ) is a popular standardised instrument typically used for screening psychopathology in children and adolescents. However, peer reviewed studies evaluating the psychometric properties of the parent-rated preschool SDQ are lacking. The current study involved mothers of 5481 2 year olds (52 % male) from the Growing Up in New Zealand cohort, and investigated the psychometric properties of the preschool SDQ within this cohort. Confirmatory factor analysis was used to evaluate the SDQ’s factor structure and test for measurement invariance of the factor model. Cronbach’s alpha was used to measure the internal consistency of the subscales and total difficulties scale. We found support for a modified five-factor model, in which the prosocial factor was extended into a positive construal factor by allowing cross-loadings of reverse-scored items. Full measurement invariance was found across gender and socioeconomic status, and partial invariance was found across mother’s ethnicity. Cronbach’s alpha was satisfactory for all subscales (α range = 0.71–0.84), except peer problems (α = 0.54). Normative scores and bandings for normal, borderline and abnormal ranges are described for each subscale. Analyses revealed group differences in scores for child’s gender, mother’s ethnicity and socioeconomic status. Overall, satisfactory psychometric properties were found for the preschool SDQ in 2 year olds, indicating that that the questionnaire can be used in very young children.