Objective The prescription of biological drugs for rheumatoid arthritis (RA) patients has varied considerably across different regions. Previous studies have shown physician preferences to be an important determinant in the decision to select biological disease-modifying anti-rheumatic drugs (bDMARDs) rather than non-biologic, synthetic DMARDs (sDMARDs) alone. The aim of this study was to test the hypothesis that physician preferences are an important determinant for prescribing bDMARDs for RA patients in Sweden. Methods Using data from the Swedish Rheumatology Quality Register, we identified 4010 RA patients who were not prescribed bDMARDs during the period 2008-2012, but who, on at least one occasion, had an sDMARD prescription and changed treatment for the first time to either a new sDMARD or a bDMARD. Physician preference for the use of bDMARDs was calculated using data on each physician's prescriptions during the study period. The relationship between prescription of a bDMARD and physician preference, controlling for patient characteristics, disease activity and the physician's local context was evaluated using multivariate logistic regression. Results When adjusting for patient characteristics, disease activity and the physician's local context, physician preference was an important predictor for prescription of bDMARDs. Compared with patients of a physician in the lowest preference tertile, patients of physicians in the highest and middle tertiles had an odds ratio for receiving bDMARD of 2.8 (95% CI 2.13-3.68) and 1.28 (95% CI 1.05-1.57), respectively. Conclusion Physician preference is an important determinant for prescribing bDMARDs. This article is protected by copyright. All rights reserved.