The measurement of breath pentane as a marker of lipid peroxidation has recently been criticized. Problems encountered include the coelution of isoprene with pentane, contamination with exogenous pentane, and the influence of elevated oxygen concentration. The aim of this project was to investigate and evaluate the Chrompack 9001 Gas Chromatograph, using thermal desorption and cryofocussing and an Al2O3/KCl PLOT column with FID, for use in the measurement of breath pentane in ventilated preterm infants. We have clearly separated isoprene from n-pentane and used hydrocarbon free air to clear the airways and avoid contamination with exogenous pentane. Samples should be stored in Tedlar bags for a maximum of 48 h and on capped desorption tubes for no longer than 24 h. Patient variability was relatively high (mean 18%, n = 4); thus, all patients were sampled in duplicate. No correlation was found between fractional inspired oxygen concentration (FiO2) and exhaled pentane in preterm infants ventilated for respiratory distress syndrome. In conclusion, we feel that despite the pitfalls and technical difficulties, with careful attention to detail it is possible to reliably measure breath pentane in ventilated preterm infants as an index of lipid peroxidation.