Institutional deprivation is multifaceted and includes adverse psychosocial and nutrition-related components. In this study we partitioned these risks in relation to cognitive impairment and mental ill health, and explored the mediating role of reduced head/brain size. There were 138 participants (61 males, 77 females) in the study. Participants were Romanian adoptees who had experienced at least 2 weeks of early institutional deprivation. The sample was stratified on the basis of duration of deprivation (high risk >6mo in institutions) and sub-nutrition (i.e. 1.5 SD below UK age-related norms for weight at UK entry). UK children adopted before 6 months of age and a group of non-institutionally deprived Romanian children constituted the comparison groups. Duration of deprivation was associated with smaller head circumference, lowered IQ, and increased mental heath problems, independently of effects found for sub-nutrition on head circumference and IQ. The mediating role of head circumference was limited to either sub-nourished (IQ) or non-sub-nourished (inattention/overactivity and disinhibited attachment) subgroups. Many negative effects of early deprivation, including stunted brain growth, occur without sub-nutrition: psychosocial deprivation plays a major role in neurodevelopmental effects of deprivation. Further studies of functional and structural neuroanatomy following institutional deprivation are required to delineate the role of brain development in its effects.