Secondary analysis of the 2007 Australian National Children’s Nutrition and Physical Activity survey was undertaken to assess the intake and food sources of EPA, DPA and DHA (excluding supplements) in 4,487 children aged 2–16 years. An average of two 24-h dietary recalls was analysed for each child and food sources of EPA, DPA and DHA were assessed using the Australian nutrient composition database called AUSNUT 2007. Median (inter quartile range, IQR) for EPA, DPA and DHA intakes (mg/day) for 2–3, 4–8, 9–13, 14–16 year were: EPA 5.3 (1.5–14), 6.7 (1.8–18), 8.7 (2.6–23), 9.8 (2.7–28) respectively; DPA 6.2 (2.2–14), 8.2 (3.3–18), 10.8 (4.3–24), 12.2 (5–29) respectively; and DHA 3.9 (0.6–24), 5.1 (0.9–26), 6.8 (1.1–27), 7.8 (1.5–33) respectively. Energy-adjusted intakes of EPA, DPA and DHA in children who ate fish were 7.5, 2 and 16-fold higher, respectively (P < 0.001) compared to those who did not eat fish during the 2 days of the survey. Intake of total long chain n-3 PUFA was compared to the energy adjusted suggested dietary target (SDT) for Australian children and 20 % of children who ate fish during the 2 days of the survey met the SDT. Fish and seafood products were the largest contributors to DHA (76 %) and EPA (59 %) intake, while meat, poultry and game contributed to 56 % DPA. Meat consumption was 8.5 times greater than that for fish/seafood. Australian children do not consume the recommended amounts of long chain omega-3 fatty acids, especially DHA, which could be explained by low fish consumption.