Objective To determine the effectiveness of helmet therapy for positional skull deformation compared with the natural course of the condition in infants aged 5-6 months.Design Pragmatic, single blinded, randomised controlled trial (HEADS, HElmet therapy Assessment in Deformed Skulls) nested in a prospective cohort study. Setting 29 paediatric physiotherapy practices; helmet therapy was administered at four specialised centres. Participants 84 infants aged 5 to 6 months with moderate to severe skull deformation, who were born after 36 weeks of gestation and had no muscular torticollis, craniosynostosis, or dysmorphic features. Participants were randomly assigned to helmet therapy (n=42) or to natural course of the condition (n=42) according to a randomisation plan with blocks of eight. Interventions Six months of helmet therapy compared with the natural course of skull deformation. In both trial arms parents were asked to avoid any (additional) treatment for the skull deformation. Main outcome measures The primary outcome was change in skull shape from baseline to 24 months of age assessed using plagiocephalometry (anthropometric measurement instrument). Change scores for plagiocephaly (oblique diameter difference index) and brachycephaly (cranioproportional index) were each included in an analysis of covariance, using baseline values as the covariate. Secondary outcomes were ear deviation, facial asymmetry, occipital lift, and motor development in the infant, quality of life (infant and parent measures), and parental satisfaction and anxiety. Baseline measurements were performed in infants aged between 5 and 6 months, with follow-up measurements at 8, 12, and 24 months. Primary outcome assessment at 24 months was blinded. Results The change score for both plagiocephaly and brachycephaly was equal between the helmet therapy and natural course groups, with a mean difference of −0.2 (95% confidence interval −1.6 to 1.2, P=0.80) and 0.2 (−1.7 to 2.2, P=0.81), respectively. Full recovery was achieved in 10 of 39 (26%) participants in the helmet therapy group and 9 of 40 (23%) participants in the natural course group (odds ratio 1.2, 95% confidence interval 0.4 to 3.3, P=0.74). All parents reported one or more side effects. Conclusions Based on the equal effectiveness of helmet therapy and skull deformation following its natural course, high prevalence of side effects, and high costs associated with helmet therapy, we discourage the use of a helmet as a standard treatment for healthy infants with moderate to severe skull deformation. Trial registration Current Controlled Trials ISRCTN18473161.