Medical journals hold an exalted position in medicine, but have many shortcomings. This perspective reviews some of the shortcomings of medical journals which are primarily related to inexperience, bias, and commercialism. The issues discussed include the uncertain mission of the traditional medical journal in the modern digital age, the inherent inexperience of voluntary editorial boards, the weaknesses and capricious nature of decisions made by the peer-review process, the uneven value of most journal articles, the bias in what gets submitted and published in journals, the misunderstanding about the criteria for authorship, the misunderstanding of the need for ethical review board approval of studies, the misunderstanding of the need for informed consent for research from patients and ethical review boards, the various sources of assistance to editors and authors in dealing with the many ethical issues arising in the publication process, the commercialization and manipulation of medical journals by industry, the prevalent and complex financial entanglements of authors with industry, and the imperfect impact factor, which has the potential to be abused. The perspective concludes with theorization of the role of medical journals in the future. Readers need to scrutinize data in the literature carefully and interpret the discussions and conclusions critically, as there are biases in what is published in medical journals.