A high ω6/ω3 ratio [fatty acid (FA) index] in the cell membrane has been associated with inadequate brain development. It has started to be used as a biomarker of treatment efficacy in human diseases. The aim of this study was to investigate if omega-3 supplementation improves erythrocyte membrane ω6/ω3, plasma antioxidant status (TAS) and autistic behaviors. A randomized, crossover, placebo-controlled study was designed to investigate the effect of 8 weeks of supplementation with ω3 (962mg/d and 1155mg/d for children and adolescents, respectively). Sixty-eight children and adolescents with Autism Spectrum Disorders (ASD) completed the full protocol. Primary outcome measures were erythrocyte membrane FA composition and TAS. Secondary outcome measures were Social Responsiveness Scale and Clinical Global Impression-Severity. Treatment with ω3 improved the erythrocyte membrane ω6/ω3 ratio (treatment effect p<0.008, d=0.66; within subjects effect p<0.007, d=0.5) without changing TAS. There was a within subjects significant improvement in Social Motivation and Social Communication subscales scores, with a moderate to large effect size (p=0.004, d=0.73 and p=0.025, d=0.79 respectively), but no treatment effect (treatment-placebo order). Carryover effects cannot be discarded as responsible for the results in behavioral measures. In conclusion, supplementation with ω3 FA might be studied as an add-on to behavioral therapies in ASD. Optimal duration of treatment requires further investigation. With regard to side effects, the effect of this supplementation on the lipid profile needs monitoring.