Background and purpose: Family physician program was implemented in Iran since 2005. The referral system is considered to be highly important in this program. But failure in appropriate implementation of referral system is a core problem of rural family medicine program in Iran. This study investigated the viewpoints of family physicians regarding referral system in 2012.

Materials and methods: This qualitative research was conducted using a conventional content analysis. Purposive sampling was done and continued until data saturation. Semi-structure interviews were carried out with 26 respondents who had at least one year experience as family physician. 

Results: Main problems were categorized as four main themes including: the role of service providers at higher levels, the role of patients, and role of executive authorities. These themes were associated with sub-themes including lack of feedback, reverse referral, patients’ lack of knowledge about the program, lack of patients’ trust in family physicians, patients who insist on receiving higher level services, and inappropriate implementation of instructions.

Conclusion: Failure in referral system in family physician program is believed to be associated either with ministry of health as the main policy-maker or the Iran Health Insurance Organization. Therefore, the policies should be reviewed or the implementation of the program should be done with more strict supervision.