Purpose: To analyze the self-citation rate (SCR) of ophthalmology journals, determine its possible effect on a journal's impact factor (IF) and compare the SCR of subspecialty journals versus general ophthalmology journals. Method: A retrospective consecutive study of ophthalmology journals listed in the Journal Citations Report (JCR) 2013. We retrieved these parameters from each journal's report: IF, total citations, self-citations, SCR and IF without self-citations (corrected IF). Results: A significant correlation was detected between the number of self-citations and publications (R2 = 86.3, p = 0.000). Subspecialty journals had a significantly higher SCR than general journals (p = 0.017). No significant difference was found in terms of IF and corrected IF between general and subspecialty journals (p = 0.260 and p = 0.108, respectively). No significant correlation between IF and SCR was detected (p = 0.099). The corrected IF was inversely correlated with SCR (R2 = -32.6, p = 0.013). An inverse correlation was detected between SCR and IF in the 29 ophthalmology journals with the lowest IF (R2 = -57.3, p = 0.001). Conclusion: Unlike other fields of medicine, the IF of an ophthalmology journal does not correlate with its SCR. Self-citation is found more often in journals with a low corrected IF and is inversely correlated with IF in the bottom half.