Objectives To determine the prevalence of conflicts of interest (COIs) among Danish physicians who are authors of clinical drug trial reports and determine the extent of undisclosed COIs in trial publications. Design Cross-sectional study. Setting The 100 most recent drug trial reports with at least one Danish non-industry employed physician author published in a journal adhering to the International Committee of Medical Journal Editors' (ICMJE) manuscript guidelines. For each article, two observers independently extracted trial characteristics and the authors' COIs. Disclosed COIs were compared to what was registered on the Danish Health and Medicines Authority's public disclosure list. Participants Trial authors who are Danish physicians. Main outcome measures Number of disclosed and undisclosed COIs. Results One observer screened 928 articles and two observers assessed 120 articles for eligibility. The 100 included trials were published from February 2011 to May 2013 and included 318 Danish non-industry employed authors. Eighty-six of the 318 authors (27%) reported one or more COIs in the journal article. We found undisclosed COIs for 40 of 318 authors (13%) related to the trial sponsor or manufacturer of trial drugs. Seventy-nine of 318 authors (25%) had undisclosed COIs related to competing companies manufacturing drugs for the same indication and 136 (43%) had undisclosed COIs with any drug manufacturer. Conclusions Almost half of all authors had undisclosed COIs in clinical trials reported in journals adhering to the International Committee of Medical Journal Editors’ manuscript guidelines. Self-declared COIs cannot be trusted, but public registries may assist editors in ensuring that more COIs are being reported.