Preclinical studies have suggested an anti-colorectal cancer effect of n-3 fatty acids, yet epidemiological studies have reported mixed results. The goal of the present meta-analysis was to examine the association between the dietary intake of n-3 fatty acids and colorectal cancer risk by conducting a meta-analysis of prospective cohort studies. We searched the PubMed database up to February 2012 to identify eligible studies. Either a fixed- or random-effects model was used to obtain a pooled relative risk (RR) comparing the highest intake of n-3 fatty acids with the lowest. We conducted subgroup analyses according to sex, geographic region, length of follow-up, cancer site and type of n-3 fatty acids. We included seven prospective studies in the meta-analysis, comprising 489 465 participants and 4656 incident cases. The pooled RR of colorectal cancer in relation to n-3 fatty acids was 0·98 (95 % CI 0·88, 1·09). The results from subgroup analysis indicated a significant reduced risk of colorectal cancer in relation to n-3 fatty acids among men (RR 0·87, 95 % CI 0·75, 1·00; n 4). No significant association was observed in other subgroups. There was no evidence of publication bias as suggested by Begg's test (P = 0·76) and Egger's test (P = 0·66). The present meta-analysis showed insufficient evidence of a protective effect of n-3 fatty acids on colorectal cancer risk. However, a reduced risk observed in men warrants further investigation.