OBJECTIVES This paper aims to evaluate disease course and outcome of patients in the first 2 years after diagnosis of juvenile idiopathic arthritis (JIA) when treated according to local standard of clinical care, focusing on achievement of inactive disease, functional ability and radiological joint damage. METHODS A retrospective inception cohort study of children with JIA, diagnosed between January 2003 and June 2007 and treated in referral centres in Amsterdam, was carried out. Disease status was determined for every outpatient-clinic visit. Data regarding medication, functional outcome and radiography were recorded. RESULTS One hundred and forty-nine consecutive newly diagnosed JIA patients were included. Median age at diagnosis was 11.8 years; median follow-up was 33 months. Synthetic DMARDs (sDMARDs) were used by 95% of patients, including methotrexate in 85%, sulfasalazine in 41% and biologics in 20%. sDMARDs were started within median 1 month after diagnosis. During follow-up, 77% of patients achieved a total of 244 episodes of inactive disease (ID). ID was reached after median 10 months. No baseline predictive factors for achievement of ID could be identified. After 2 years a median CHAQ score of 0.6 was reported. Radiological joint damage occurred at some point in 18 patients (12%); 10 of these patients developed erosions within median 20 months after their first clinic visit. CONCLUSIONS With current management strategies in daily clinical practice, 77% of newly diagnosed JIA patients achieved a first episode of inactive disease within a median of 10 months. After 2 years, patients reported moderate functional disability and more than 10% showed radiological evidence of joint damage.