Objective. The Veterans Affairs (VA) Rheumatoid Arthritis (VARA) registry and the VA Pharmacy Benefits Management database were linked to determine the association of methotrexate (MTX) adherence with rheumatoid arthritis (RA) disease activity. Methods. For each patient, the medication possession ratio (MPR) was calculated for the first episode of MTX exposure of a duration of ≥12 weeks for both new and established MTX users. High MTX adherence was defined as an MPR ≥0.80 and low MTX adherence was defined as an MPR <0.80. For each patient, the mean Disease Activity Score with 28 joints (DAS28) score, erythrocyte sedimentation rate (ESR), and C-reaction protein (CRP) level observed during registry followup were compared in high-versus low-adherence groups. Results. In 455 RA patients, the prescribed doses of MTX (mean ± SD 16 ± 4 mg versus 16 ± 4 mg; P = 0.6) were similar in high-adherence patients (n = 370) in comparison to low-adherence patients (n = 85). However, the actual observed MTX doses taken by patients were significantly higher in the high-adherence group (mean ± SD 16 ± 5 mg versus 11 ± 3 mg; P < 0.001). DAS28 (mean ± SD 3.6 ± 1.2 versus 3.9 ± 1.5; P < 0.02), ESR (mean ± SD 24 ± 18 versus 29 ± 24 mm/hour; P = 0.05), and CRP level (mean ± SD 1.2 ± 1.3 versus 1.6 ± 1.5 mg/dl; P < 0.03) were lower in the high-adherence group compared to those with low MTX adherence. These variances were not explained by differences in baseline demographic features, concurrent treatments, or whether MTX was initiated before or after VARA enrollment. Conclusion. High MTX adherence was associated with improved clinical outcomes in RA patients treated with MTX. Adjustment for potential confounders did not alter the estimated effect of adherence. These results demonstrate the advantages of being able to merge clinical observations with pharmacy databases to evaluate antirheumatic drugs in clinical practice. © 2011, American College of Rheumatology.