For the past 25 years, the structure of academic research papers has been examined by linguists. In the present study, the functions of references in discussion and conclusion sections of academic research papers were explored using a modified version of moves and steps outlined in Swales (1990). References in 12 disciplines of the annotated Iowa State University Academic Writing Corpus were examined for their frequency. The highest frequency disciplines were further investigated to find out the functions of the references, how these vary within and across disciplines, and what patterns exist in regards to the contextual location of references. Biology stood out with extensive use of references for empirical background, while information systems and engineering were characterized by fewer, mostly “uncited” references. Variation in function was found within disciplines, yet discipline–specific characteristics emerged. The findings could be used in graduate–level writing courses to raise awareness of discipline–specific tendencies. Differences in function were found to exist depending on the level of context taken into account, pointing to a need for specificity in research on functional moves. The results also support the notion that a multi–level, move–step analysis is best suited for structural descriptions of discussion and conclusion sections.