The organization of scientific papers typically follows a standardized pattern, the well-known IMRaD structure (introduction, methods, results, and discussion). Using the full text of 45,000 papers published in the PLoS series of journals as a case study, this paper investigates, from the viewpoint of bibliometrics, how references are distributed along the structure of scientific papers as well as the age of these cited references. Once the sections of articles are realigned to follow the IMRaD sequence, the position of cited references along the text of articles is invariant across all PLoS journals, with the introduction and discussion accounting for most of the references. It also provides evidence that the age of cited references varies by section, with older references being found in the methods and more recent references in the discussion. These results provide insight into the different roles citations have in the scholarly communication process.