In children undergoing total parenteral nutrition (PN), lipids provide a key source of calories preventing or correcting energy deficits and improving outcomes. However, some of these lipids may undergo oxidation leading to the formation of malondialdehyde (MDA), a cytotoxic byproduct found in these patients. This paper aims to describe a sensitive method for detecting MDA and discuss its role in certain diseases commonly found in children on regular PN. To quantify MDA levels in children benefitting from long-term cyclic PN, a reliable and sensitive high-performance liquid chromatographic method based on a 1-step derivatization/extraction procedure analysis with ultraviolet determination at 305 nm wavelength was achieved. In control children without PN, MDA levels were on average 3.30 ± 0.08 μM. However, in children nourished intravenously by fat emulsion for a long time, in which liver problems have been identified, the circulating concentrations of MDA ranged widely at both the start and the end of a session, 3- to 10-fold, respectively, in comparison with the levels measured in controls. This finding indicates that PN administrated long term raises plasma MDA levels, indicating chronic exposure and therefore a possible health risk, particularly liver damage. This preliminary study using a limited number of patients and controls showed that children undergoing long-term PN are strongly exposed to MDA, which must be considered as a potent toxic compound rather than a simple marker of lipid peroxidation.