The purpose of this study was to assess the degree of editorial independence at a sample of medical journals and the relationship between the journals and their owners. We surveyed the editors of 33 medical journals owned by not-for-profit organizations ("associations"), including 10 journals represented on the International Committee of Medical Journal Editors (nine of which are general medical journals) and a random sample of 23 specialist journals with high impact factors that are indexed by the Institute for Scientific Information. The main outcome measures were the authority to hire, fire, and oversee the work of the editor; the editor's tenure and financial compensation; control of the journal's budget; publication of material about the association; and the editor's perceptions about editorial independence and pressure over editorial content. Of the 33 editors, 23 (70%) reported having complete editorial freedom, and the remainder reported a high level of freedom (a score of > or = 8, where 10 equals complete editorial freedom and 1 equals no editorial freedom). Nevertheless, a substantial minority of editors reported having received at least some pressure in recent years over editorial content from the association's leadership (42%), senior staff (30%), or rank-and-file members (39%). The association's board of directors has the authority to hire (48%) or fire (55%) the editor for about half of the journals, and the editor reports to the board for 10 journals (30%). Twenty-three editors (70%) are appointed for a specific term (median term = 5 years). Three-fifths of the journals have no control over their profit, and the majority of journals use the association's legal counsel and/or media relations staff. Stronger safeguards are needed to give editors protection against pressure over editorial content, including written guarantees of editorial freedom and governance structures that support those guarantees. Strong safeguards are also needed because editors may have less freedom than they believe (especially if they have not yet tested their freedom in an area of controversy).