The editors of the Journal of Biological Chemistry have criticized the modern reliance upon the impact factor for ranking journals, noting that review articles, commentaries, and retractions are included in the calculation. Further, the denominator of total articles published encourages journals to be overly selective in what they publish, and preferentially publish articles which will receive more attention and citations.

Due to these factors, the journal's practice of publishing a broad cross-section of biochemistry articles has led it to suffer in impact factor, in 2006 ranking 260 of 6,164, while remaining a highly cited journal.[4] When science journals were evaluated with a PageRank-based algorithm, however, the Journal of Biological Chemistry ranked first.

Using the Eigenfactor metric, considered to be a more robust alternative to the impact factor, the Journal of Biological Chemistry ranked 5th among all ISI-indexed journals in 2010.