The increasing number of journals makes it difficult to decide the right venue for manuscript submission. This becomes more complicated as the selection criteria may vary from one discipline to another. Therefore, appropriate cross‐disciplinary studies are required to understand the exact concerns that dominate a particular field. The current study compares 16 factors that influence journal choices between medicine and social sciences using the answers given to a global survey of 235 open access journal authors. The results reveal that authors of both areas consider ‘peer reviewed’ status as the most important factor while showing the least interest to the ‘number of annual subscribers’ of the journal. However, compared to social science authors, those in the discipline of medicine give significantly more consideration to (1) impact factor, (2) the inclusion of the journal in abstracting and indexing services, (3) publisher's prestige, and (4) online submission with tracking facility. The factors that were identified can be categorized for both disciplines as reflecting the reputation of a journal, performance or production issues, and reliability and demand characteristics of their publication choice. The editors and publishers can use these findings to attract the best manuscripts as the study reveals the author's perception of the journal's status. The results can also be used to design recommender systems for journal submission for new authors in a discipline.