We investigated the age-related changes in the metabolic profile of male Drosophila melanogaster and compared the metabolic profile of flies selected for increased longevity to that of control flies of equal age. We found clear differences in metabolite composition between selection regimes and among age groups. Contrary to results found in a previous study of the transcriptome of these lines the metabolic profile did not show a younger pattern in longevity-selected (LS) flies than in same aged control (C) flies. Rather, many of the metabolites affected by age had levels common to older control individuals in the young LS flies. Furthermore, ageing affected the metabolome in a different LS specific direction. The selection induced difference increased with age. Some metabolites involved in oxidative phosphorylation changed with age highlighting the importance of mitochondrial function in the ageing process. However, these metabolites were not affected by selection for increased longevity, indicating that improvements of mitochondrial function were not involved in the increased lifespan of LS lines. Of the eight metabolites identified as having a significant difference in relative abundance between selection regimes in our study choline, lysine and glucose also show difference among lifespan phenotypes in C. elegans indicating that the correlation between the concentration of these metabolites and longevity was evolutionary conserved. Links between longevity and choline concentration is also found in mice making this metabolite an obvious target for further study.