Importance It is unclear how medical journals address authors’ financial and non-financial conflict of interest (COI). Objective To assess the policies of clinical journals for disclosure of financial and non-financial COI. Methods Cross sectional study that included both review of public documents as well as a simulation of a manuscript submission for the National Library of Medicine’s “core clinical journals”. The study did not involve human subjects. Investigators who abstracted the data, reviewed “instructions for authors” on the journal website and, in order to reflect the actual implementation of the COI disclosure policy, simulated the submission of a manuscript. Two individuals working in duplicate and independently to abstract information using a standardized data abstraction form, resolved disagreements by discussion or with the help of a third person. Results All but one of 117 core clinical journals had a COI policy. All journals required disclosure of financial COI pertaining to the authors and a minority (35%) asked for financial COI disclosure pertaining to the family members or authors' institution (29%). Over half required the disclosure of at least one form of non-financial COI (57%), out of which only two (3%) specifically referred to intellectual COI. Small minorities of journals (17% and 24% respectively) described a potential impact of disclosed COI and of non-disclosure of COI on the editorial process. Conclusion While financial COI disclosure was well defined by the majority of the journals, many did not have clear policies on disclosure of non-financial COI, disclosure of financial COI of family members and institutions of the authors, and effect of disclosed COI or non-disclosure of COI on editorial policies.