Industry sponsored drug and device studies more often had favorable efficacy results, (risk ratio (RR): 1.24, 95% confidence interval (CI): 1.14 to 1.35), harms results (RR: 1.87, 95% CI: 1.54 to 2.27) and overall conclusions (RR: 1.31, 95% CI: 1.20 to 1.44), compared with non-industry sponsored drug and device studies. We did not find a difference between industry and non-industry sponsored studies with respect to standard factors that may increase the risk of bias, except for blinding: industry sponsored studies reported satisfactory blinding more often than non-industry sponsored studies. We did not find a difference between drug and device studies on the association between sponsorship and conclusions. In industry sponsored studies, there was less agreement between the results and the conclusions than in non-industry sponsored studies, RR: 0.84 (95% CI: 0.70 to 1.01). Our analysis suggests that industry sponsored drug and device studies are more often favorable to the sponsor’s products than non-industry sponsored drug and device studies due to biases that cannot be explained by standard ‘Risk of bias’ assessment tools.