Background: One of the disadvantages of the Impact Factor (IF) is self-citation. The SCImago Journal Rank (SJR) indicator excludes self-citations and considers the quality, rather than absolute numbers, of citations of a journal by other journals. The present study re-evaluated the influence of self-citation on the 2007 IF for 18 major orthopaedic journals and investigated the difference in ranking between IF and SJR. Methods: The journals were analysed for self-citation both overall and divided into a general group (n = 8) and a specialized group (n = 10). Self-cited and self-citing rates, as well as citation densities and IFs corrected for self-citation (cIF), were calculated. The rankings of the 18 journals by IF and by SJR were compared and the absolute difference between these rankings (Delta R) was determined. Results: Specialized journals had higher self-citing rates (p = 0.01, Delta median = 9.50, 95%CI-19.42 to 0.42), higher self-cited rates (p = 0.0004, Delta median = -10.50, 95% CI-15.28 to -5.72) and greater differences between IF and cIF (p = 0.003, Delta median = 3.50, 95%CI -6.1 to 13.1). There was no significant correlation between self-citing rate and IF for both groups (general: r = 0.46, p = 0.27; specialized: r = 0.21, p = 0.56). When the difference in ranking between IF and SJR was compared between both groups, sub-specialist journals were ranked lower compared to their general counterparts (Delta R: p = 0.006, Delta median = 2.0, 95% CI -0.39 to 4.39). Conclusions: Citation analysis shows that specialized orthopaedic journals have specific self-citation tendencies. The correlation between self-cited rate and IF in our sample was large but, due to small sample size, not significant. The SJR excludes self-citations in its calculation and therefore enhances the underestimation in ranking of specialized journals.