We sought to compare the Eigenfactor Score™ journal rank with the journal Impact Factor over five years, and to identify variables that may influence the ranking differences between the two metrics. Datasets were retrieved from the Thomson Reuters® and Eigenfactor Score™ Web sites. Dentistry was identified as the most specific medical specialty. Variables were retrieved from the selected journals to be included in a regression linear model. Among the 46 dental journals included in the analysis, striking variations in ranks were observed according to the metric used. The Bland-Altman plot showed a poor agreement between the metrics. The multivariate analysis indicates that the number of original research articles, the number of reviews, the self-citations, and the citing time may explain the differences between ranks. The Eigenfactor Score™ seems to better capture the prestige of a journal than the Impact Factor. In medicine, the bibliometric indicators should focus not only on the overall medical field but also on specialized disciplinary fields. Distinct measures are needed to better describe the scientific impact of specialized medical publications.