Factors relevant to the discordance between the patient global assessment (PGA) and estimator global assessment (EGA) in patients newly diagnosed with rheumatoid arthritis (RA) were examined. Seventy-five consecutive newly diagnosed patients with RA were prospectively enrolled. We used 3 models in which discordance between PGA and EGA at 12 months was set at 5 mm, 10 mm, or 20 mm. We adopted 10 mm as representative and examined time course changes in clinical variables over 12 months. No significant difference was found between the concordance and the higher PGA groups regarding baseline characteristics and treatment. At 12 months, EGA, swollen joint count, and inflammatory marker values were not different, but pain visual analog scale and tender joint count were significantly higher in the higher PGA group, and the Health Assessment Questionnaire improved less. In the 10 mm and 20 mm models, the structural remission rate was significantly lower in the higher PGA group and the rapid radiological progression rate significantly higher. The discrepancy was already significant at 3 months. In newly diagnosed RA, PGA at 12 months may be more sensitive for indicating progressive joint destruction and functional impairment when compared with EGA, and there is a discrepancy directed toward a worse assessment by patients.