Background This study aimed to clarify the factors underlying the discrepancy that has been noted between estimated glomerular filtration ratio (eGFR) measured using serum creatinine (Cr) and eGFR using serum cystatin C (CysC) in patients with rheumatoid arthritis (RA) and to identify those patients whose renal function should be evaluated using CysC.Methods We retrospectively evaluated clinical features, disease activity, radiological grading, and co-morbidities (diabetes mellitus, hypertension, dyslipidemia) in 238 RA patients. eGFR using serum creatinine (eGFR-Cr) and eGFR using serum cystatin C (eGFR-CysC) were calculated using the new Japanese coefficient-modified Modification of Diet in Renal Disease study equation. To clarify the cause(s) of differences of 20% or more between the two eGFRs, we divided our RA patients into Group A (eGFR-Cr/eGFR-CysC ≥ 1.2), with eGFR-Cr more than 20% higher than eGFR-CysC, and Group B (eGFR-Cr/eGFR-CysC < 1.2), and compared various clinical parameters between them.Results Forty-five patients (18.9%) were assigned to Group A, and 193 (81.1%) to Group B. Group A were older (73.8 ± 12.5 vs 63.2 ± 13.6 years), and had a longer disease duration (17.7 ± 14.0 vs 10.4 ± 9.5 years), lower body mass index (BMI) (20.0 ± 2.9 vs 22.4 ± 3.6 kg/m2), higher frequencies of hypertension and diabetes mellitus (55.6% vs 30.1% and 35.6% vs 11.0%, respectively), higher DAS28-ESR (3.1 ± 1.3 vs 2.6 ± 1.0), lower hemoglobin (Hb) (11.8 ± 1.8 vs 12.8 ± 1.4 g/dl), lower creatine kinase (CK) (63.9 ± 36.0 vs 92 ± 79 IU/L), higher frequency of Steinbrocker stage 4 (46.7% vs. 15.3%), and a lower frequency of nonsteroidal anti-inflammatory drugs (NSAID) use (13.3% vs 30.6%), all significantly (p < 0.01) by a univariate analysis. BMI (Odds Ratio [OR] 0.820, 95% confidence interval [CI] 0.675–0.996), Hb (OR 0.633, 95% CI 0.433–0.926), CK (OR 0.773 per 10 units, 95% CI 0.644–0.933), NSAID use (OR 0.099, 95% CI 0.020–0.494), diabetes mellitus (OR 6.024, 95% CI 1.508–24.390) and stage 4 Steinbrocker radiological grade (OR 10.309, 95% CI 2.994–35.714) were identified as independent relevant factors for Group A by a multifactorial analysis.Conclusion Renal function in RA patients with low BMI, diabetes, anemia and low CK may be overestimated using eGFR-Cr alone, and such patients need to be evaluated using eGFR-CysC.