Abstract Background Researchers paid little attention to understanding the association of organizational and human factors with patients’ perceived security in the context of health organizations. This study aims to address numerous gaps in this context. Patients’ perceptions about employees’ training on security issues, monitoring on security issues, ethics, physical & technical protection and trust in hospitals were identified as organizational and human factors. Methods After the development of 12 hypotheses, a quantitative, cross-sectional, self-administered survey method was applied to collect data in 9 hospitals in Iran. After the collection of 382 usable questionnaires, the partial least square structural modeling was applied to examine the hypotheses and it was found that 11 hypotheses were empirically supported. Results The results suggest that patients’ trust in hospitals can significantly predict their perceived security but no significant associations were found between patients’ physical protection mechanisms in the hospital and their perceived information security in a hospital. We also found that patients’ perceptions about the physical protection mechanism of a hospital can significantly predict their trust in hospitals which is a novel finding by this research. Conclusions The findings imply that hospitals should formulate policies to improve patients’ perception about such factors, which ultimately lead to their perceived security.