Both protein-energy malnutrition (PEM) and obesity represent major challenges for paediatric nutrition. The aim of this review is to summarise available data regarding the effect of PEM and obesity on the availability of essential- and long-chain polyunsaturated fatty acids (LC-PUFAs) in childhood. Significantly lower arachidonate (C20:4n-6, AA) values in malnourished children than in controls is a consistent finding in all studies, whereas it is controversial whether the availability of docosahexaenoate (C22: 6n-3, DHA) is also affected. We found significantly lower percentages (% wt/wt) of both AA and DHA in plasma phospholipids [AA: 7.0 (0.7) vs 8.7 (0.8); DHA: 0.90 (0.2) vs 2.6 (0.7), median (interquartile range), P < 0.001] in severely malnourished children aged 29 (7) months than in control subjects. Product/substrate ratios indicated reduced delta-5-desaturation in children with PEM. We speculate that severely malnourished children may benefit from enhanced dietary supply of both n-6 and n-3 LC-PUFAs. In obese adults AA has been reported to constitute a lower percentage of plasma phospholipid fatty acids, and AA supplementation of weight reduction diets has been suggested. In contrast, we found significantly higher plasma phospholipid AA values [12.6 (2.4) vs 8.3 (1.4), P < 0.001] in markedly obese children aged 13.8 (1.1) years than in non-obese controls. Product/substrate ratios of the delta-6-desaturase enzyme indicated enhanced conversion activity. These data suggest that obese children do not require LC-PUFA supplementation to low fat diets. The available data indicates that both PEM and obesity alter fatty acid composition of plasma and erythrocyte membrane lipids. The underlying mechanism appears to be altered activity of the bioconversion of essential fatty acids to their LC-PUFA metabolites.