Background: The present study aimed to develop a food frequency questionnaire (FFQ) assessing dietary omega-3 long chain polyunsaturated fatty acid (n-3 LCPUFA) intake in Australian children and to validate the FFQ against a 7-day food diary. Methods: The investigation comprised a cross-sectional and validation study. The study setting was two private primary schools in the in the Illawarra region of New South Wales. Twenty-two Australian children, aged 9-13 years, who were not on a special diet or receiving medical care that limited their food choice in the 3 months prior to recruitment, were recruited into the study. Results: A total of 131 items, classified according to seven food group categories, was included in the n-3 LCPUFA FFQ, as identified from published dietary surveys and a supermarket survey. Good correlations between the FFQ and the 7-day food diary were observed for eicosapentaenoic acid (EPA) [r = 0.691, 95% confidence interval (CI) = 0.51-0.83, P < 0.001], docosahexaenoic acid (DHA) (r = 0.684, 95% CI = 0.45-0.84, P < 0.001) and total n-3 LCPUFA (r = 0.687, 95% CI = 0.48-0.85, P < 0.001). Bland-Altman plots showed an acceptable limit of agreement between the FFQ and the average 7-day food diary. However, the mean EPA, DHA and total n-3 LCPUFA intakes estimated from the FFQ were significantly higher than those from the average 7-day food diary estimates (P < 0.001). Conclusions: A novel n-3 LCPUFA FFQ that has been developed to estimate dietary n-3 LCPUFA intakes in Australian children has been shown to have relative validity. The FFQ provides a useful contribution to dietary assessment methodology in this age group; however, reproducibility remains to be demonstrated.