Objectives To determine the role of academic authors, funders, and contract research organisations in industry funded trials of vaccines, drugs, and devices and to determine lead academic authors’ experiences with industry funder collaborations. Design Cross sectional analysis of trial publications and survey of lead academic authors. Eligibility criteria for selecting studies The most recent 200 phase III and IV trials of vaccines, drugs, and devices with full industry funding, at least one academic author, published in one of the top seven high impact general medical journals (New England Journal of Medicine, Lancet, JAMA, BMJ, Annals of Internal Medicine, JAMA Internal Medicine, and PLoS Medicine). Results Employees of industry funders co-authored 173 (87%) of publications; 183 (92%) trials reported involvement of funders in design, and 167 (84%) reported involvement of academic authors. Data analysis involved the funder in 146 (73%) trials and the academic authors in 79 (40%). Trial reporting involved the funder in 173 (87%) trials and academic authors in 197 (99%). Contract research organisations were involved in the reporting of 123 (62%) trials.Eighty (40%) of 200 lead academic authors responded to the survey. Twenty nine (33%) of the 80 responders reported that academics had final say on the design. Ten responders described involvement of an unnamed funder and/or contract research organisation employee in the data analysis and/or reporting. Most academic authors found the collaboration with industry funder beneficial, but 3 (4%) experienced delay in publication due to the industry funder and 9 (11%) reported disagreements with the industry funder, mostly concerning trial design and reporting. Conclusions Industry employees and academic authors are involved in the design, conduct, and reporting of most industry funded trials in high impact journals. However, data analysis is often conducted without academic involvement. Academics view the collaboration as beneficial, but some report loss of academic freedom.