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Background  Autism spectrum disorder (ASD) is a neurodevelopmental disorder affecting more than 1% of children. It is characterized by social communication deficits and repetitive behaviors/restricted interests. In the absence of any medications known to improve core symptom domains, parents often use complementary alternative treatments, including omega-3 fatty acid supplements.    Methods  We conducted a 6-month, randomized, placebo controlled trial of omega-3 fatty acid supplements (1.5 g) vs placebo in children 2 to 5 years of age with ASD. Primary outcome measures included the autism composite score of the Pervasive Developmental Disorders Behavioral Inventory (PDDBI) and the externalizing problems score of the Behavior Assessment System for Children (BASC-2). Secondary outcome measures included clinical global improvement (Clinical Global Impression-Improvement (CGI-I)), adaptive function (Vineland Adaptive Behavior Scale (VABS-II)), and language gains (Preschool Language Scale (PLS-4)), as well as safety. Exploratory analysis investigated potential correlations between changes in cytokine profiles and treatment response.    Results  Thirty-eight participants were randomized in a 1:1 fashion. There was no significant difference between groups on the 0- to 24-week change in PDDBI autism composite scores ( p  = 0.5). There was a significant group by week interaction on the BASC-2 externalizing problem score, with participants randomized to the treatment group demonstrating worsening scores ( p  = 0.02). There was no statistically significant week by group effect on either adaptive function ( p  = 0.09) or language ( p  = 0.6). Omega-3s were relatively well tolerated. Changes in cytokines during the study did not significantly correlate with treatment response.    Conclusions  This study does not support high dose supplementation of omega-3 fatty acids in young children with ASD.    Trial registration  Clinicaltrials.gov  NCT01248728 . Registered 22 November 2010.    Electronic supplementary material  The online version of this article (doi:10.1186/s13229-015-0010-7) contains supplementary material, which is available to authorized users.

A randomized, placebo controlled trial of omega-3 fatty acids in the treatment of young children with autism