Introduction: Omega-3 Polyunsaturated Fatty Acids (PUFAs) play an important role in developing cognitive function in children, especially Docosahexanoic Acid (DHA). However, there is no suitable dietary assessment tool to assess DHA intake among Malaysian children. Thus, this study assessed the validity of an interviewer-administered semi-quantitative Food Frequency Questionnaire (FFQ) for estimating DHA intake among Malay school children in the Sepang District. Methods: Thirty 12-year-old Malay children (13 boys and 17 girls) were recruited through purposive sampling. Their DHA intake for one month duration was assessed using a 30-food item FFQ and validated against a 3-day food record. Results: The majority of the subjects (70%) had normal body mass index, 6.7% were overweight, 16.7% obese, whilst the rest were in the thin category. The reliability of FFQ was found to be good with a Cronbach’s α coefficient value of 0.815. Wilcoxon Signed Rank Test indicated no significant difference in mean intake between the two assessment methods. Significant and strong correlation between FFQ and the 3-day food record was found for total omega-3 PUFAs (r=0.812)and DHA (r=0.839) using both methods. Bland Altman analysis exhibited no apparent systematic bias between the two methods for DHA and total omega-3 PUFAs intake, whilst a quartile analysis assigned 73.3% of the subjects into the same quartile. Conclusion: The FFQ was found to be valid in estimating DHA intake among Malay school children, and it is recommended that its validity be tested on other ethnic population groups.