Background: There is conflicting evidence on the use of omega 3 and omega 6 supplementation for the prevention of allergic diseases. We conducted a systematic review evaluating the effectiveness of omega 3 and 6 oils for the primary prevention of sensitization and development of allergic disorders.Methods: We searched The Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, LILACS, PsycInfo, AMED, ISI Web of Science and Google Scholar for double‐blind randomized controlled trials. Two authors independently assessed articles for inclusion. Meta‐analyses were undertaken using fixed effects modelling, or random effects modelling in the event of detecting significant heterogeneity.Results: Of the 3129 articles identified, 10 reports (representing six unique studies) satisfied the inclusion criteria. Four studies compared omega 3 supplements with placebo and two studies compared omega 6 supplements with placebo. There was no clear evidence of benefit in relation to reduced risk of allergic sensitization or a favourable immunological profile. Meta‐analyses failed to identify any consistent or clear benefits associated with use of omega 3 [atopic eczema: RR = 1.10 (95% CI 0.78–1.54); asthma: RR = 0.81 (95% CI 0.53–1.25); allergic rhinitis: RR = 0.80 (95% CI 0.34–1.89) or food allergy RR = 0.51 (95% CI 0.10–2.55)] or omega 6 oils [atopic eczema: RR = 0.80 (95% CI 0.56–1.16)] for the prevention of clinical disease.Conclusions: Contrary to the evidence from basic science and epidemiological studies, our systematic review and meta‐analysis suggests that supplementation with omega 3 and omega 6 oils is probably unlikely to play an important role as a strategy for the primary prevention of sensitization or allergic disease.