Objective of the study is to investigate how compliance during the first year of methotrexate (MTX) treatment in rheumatoid arthritis (RA) is influenced by the patients' perception of the necessity for and concern about MTX, the patients' functional disability, and the dose of MTX. A total of 126 RA patients completed a questionnaire at start of MTX treatment and after 9 months. The MTX compliance was measured by using the Compliance Questionnaire Rheumatology (CQR). The prevalence of having a CQR score in the bottom quartile was stratified according to age, gender, the duration of RA, MTX dose, years of school education, functional disability, use of folic acid, and co-morbidity. Crude and adjusted prevalence ratios (PR) with 95% confidence intervals (CI) were calculated by using log-binomial regression. The necessity and concern scales of the Beliefs about Medication Questionnaire were dichotomised into high perception of MTX necessity and low concern about MTX treatment, and the crude and adjusted PR of having a CQR score in the bottom quartile were estimated. The prevalence of having a CQR in the bottom quartile was 23%, both at baseline and after 9 months, and this finding was not associated with the MTX dose level or the patients' functional disability. Among patients with a CQR in the bottom quartile, the prevalence of having low perceptions of MTX necessity was 37.1 versus 14.0% for patients with high perceptions of necessity [adjusted PR: 0.3 (95% CI 0.2-0.8)]. The same tendency was seen after 9 months. The prevalence of having a CQR in the bottom quartile or not was almost equally distributed among patients who had high or low concerns about treatment at baseline. After 9 months, however, the prevalence of having a CQR in the bottom quartile was 18.9% for patients who had low concerns about the MTX treatment, versus 37.7% for patients who had higher concerns about the treatment [adjusted PR: 0.5 (95% CI 0.2-1.3)]. During the first year of treatment, compliance with MTX treatment among RA patients could be explained by strong perceptions of a personal need for the treatment. Compliance did not seem to be influenced by the patients' functional impairment or the MTX dose level.