Aim. The aim of the study was to assess associations between minor neurological dysfunction (MND) and behaviour, with specific attention to sex differences. Method. This was an observational cohort study in which 341 9-year-old children (177 male, 164 female) without perinatal risk were neurologically assessed, with attention to severity and type of MND. Eight domains of dysfunction were distinguished, including posture and muscle tone, fine manipulative ability and coordination. Severity of MND was based on the number of dysfunctional domains. Behaviour was assessed by parents and teachers using the Child Behavior Checklist and Teacher's Report Form (TRF); outcomes were internalizing and externalizing behaviour and total score of behavioural problems. Results. Females with complex MND or dysfunctional posture and muscle tone had increased risk for externalizing behavioural problems (OR 4.52, 95% CI 1.01–20.2, and OR 4.05, 95% CI 1.06–15.5, respectively). In males, these associations were absent. However, males with simple MND had an increased risk for behavioural problems indicated by the total TRF-score (OR 7.52, 95% CI 1.36–41.4). Interpretation. In children without perinatal risk, associations between MND and behaviour are sex-specific. In females, dysfunction of complex neural networks, including the cerebellum, is associated with externalizing behaviour. In males, neurobehavioural relationships are limited, suggesting a larger role of psychosocial factors in the genesis of behavioural problems.