Purpose: Rheumatoid arthritis (RA) is a chronic multi-systemic disease that causes damage to the bone and connective tissues. This study was conducted in order to accurately measure the correlation between RA and periodontitis, and to obtain an unbiased estimate of the effect of RA on periodontal indices. Methods: In this historical cohort study, which was conducted from February to May 2011 in Hamadan city, Iran, 53 exposed people (with RA) were compared with 53 unexposed people (without RA) in terms of clinical periodontal indices (the outcomes of interest) including 1) plaque index (PI), 2) bleeding on probing (BOP), and 3) clinical attachment loss (CAL). Results: A sample of 106 volunteers were evaluated, 53 rheumatoid versus 53 non-rheumatoid subjects. There was a statistically significant correlation between RA and BOP (P<0.001) and between RA and CAL (P<0.001). However, there was no statistically significant correlation between RA and any of the periodontal indices. No correlation was seen between gender and any of the indices either. There was a strong positive correlation between age and all three periodontal indices (P<0.001). Conclusions: The present study indicated a potential effect of RA on periodontal indices. However, much more evidence based on a prospective cohort study is needed to support the cause and effect relationship between RA and periodontal indices.