In recent years advances in quantitative trait loci (QTL) mapping of complex metabolomics traits have been made in plants. This study is a two-phase experiment in which we have profiled transesterified non-polar metabolites in a Lolium perenne population consisting of parents, F1 and 325 F2 genotypes. These were grown in a replicated field trial, then analysed in batches by a targeted approach using gas-chromatography mass spectrometry (GC-MS), which identified 17 metabolites. The metabolite data was analysed using a mixed model that included random effects of field replicate, laboratory batch and technical replication to derive genotype means for QTL mapping. Using a linkage map of 326 markers, mainly Diversity Array Technology markers, QTLs were detected for seven of the metabolites. The most heritable metabolite was octacosanol, where a single QTL on linkage group four explained 42 % of the trait variance.