The relationships between n-3 and n-6 fatty acids in subcutaneous fat, BMI and overweight status were investigated in eighty-eight children from Crete and Cyprus. Overweight status, BMI and serum lipid levels were similar in children at both locations, but Cretan children had higher levels of total MUFA than Cypriot children (62·2 (sd 2·8) v. 52·2 (sd 2·8)% area, respectively, P<0·001) and consequently Cypriot children had higher levels of total saturated, polyunsaturated, trans, n-3 and n-6 fatty acids. Cypriot children had also higher levels of individual n-3 and n-6 fatty acids, specifically linoleic, α-linolenic and dihomo-γ-linolenic acids. The variance of BMI was better explained (38·2%) by adipose tissue arachidonic acid content than any other n-3 and n-6 fatty acids. Mean levels of arachidonic acid, dihomo-γ-linolenic acid and docosahexaenoic acid were higher in overweight and obese subjects. All obese subjects fell in the 4th quartile of arachidonic acid levels, whereas 88·9% of overweight subjects fell in the 3rd and 4th quartile of arachidonic acid. These results indicate positive associations between adipose tissue arachidonic acid and BMI and overweight status. Further research could clarify whether this association is causal.