In a prospective longitudinal study, we investigated the outcomes of children born to mothers clinically referred for mental health problems during pregnancy (risk group, n = 17) relative to a control group (n = 31). Child cognitive functioning, and for subgroups (n = 10 + 17), brain morphometry as derived from Magnetic resonance imaging (MRI), was measured at 4½ years. Cognitive data included abstract visuospatial reasoning/problem solving and verbal scores. Subcortical regions of interest included the amygdala, accumbens area, hippocampus, caudate and putamen, chosen because their development seems potentially sensitive to an adverse intrauterine milieu and environmental experiences, and also due to their implication in cognitive and emotional processes. The risk group exhibited poorer abstract reasoning scores than the control group. No differences were found for verbal scores. MRI revealed smaller putamen volume in children in the risk group. Irrespective of group, putamen volume was positively related to visuospatial reasoning performance. Our results suggest that maternal psychopathology may be associated with child putamen development, nonverbal reasoning and problem solving skills.