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Journals play a critical role in the scientific process because they evaluate the quality of incoming papers and offer an organizing filter for search. However, the role of journals has been called into question because new preprint archives and academic search engines make it easier to find articles independent of the journals that publish them. Research on this issue is complicated by the deeply confounded relationship between article quality and journal reputation. We present an innovative proxy for individual article quality that is divorced from the journal's reputation or impact factor: the number of citations to preprints posted on arXiv.org. Using this measure to study three subfields of physics that were early adopters of arXiv, we show that prior estimates of the effect of journal reputation on an individual article's impact (measured by citations) are likely inflated. While we find that higher‐quality preprints in these …