Scholarly references join journals together in a vast network of citations. The Eigenfactor algorithm uses the structure of the entire network (instead of purely local citation information) to evaluate the importance of each journal.

In collaboration with journalprices.com, Eigenfactor provides information about price and value for thousands of scholarly periodicals. While the Eigenfactor and Article Influence scores do not incorporate price information directly, the Cost-Effectiveness Search orders journals by a measure of the value per dollar that they provide.

Eigenfactor not only ranks scholarly journals in the natural and social sciences, but also lists newsprint, PhD theses, popular magazines and more. In so doing, it more fairly values those journals bridging the gap between the social and natural sciences.

Different disciplines have different standards for citation and different time scales on which citations occur. The average article in a leading cell biology journal might receive 10-30 citations within two years; the average article in leading mathematics journal would do very well to receive 2 citations over the same period. By using the whole citation network, the Eigenfactor algorithm automatically accounts for these differences and allows better comparison across research areas.

In many research areas, articles are not frequently cited until several years after publication. Therefore, measures that only look at citations in the first two years after publication can be be misleading. The Eigenfactor score is calculated based on the citations received over a five year period.