To improve the quality of research, it is necessary to understand the obstacles to undertaking research. This study aimed to identify i) internal obstacles to research as considered by faculty members at Shiraz University of Medical Sciences; ii) differences between their viewpoints by gender and professional variables; and iii) the effect of these obstacles on research activity. Six types of obstacle were considered financial, facility-related, occupational, managerial–organizational, scientific and personal. The study sample consisted of 240 participants selected from all 550 faculty members of the University. Data were collected by self-administered questionnaire; the response rate was 91%. All 6 types of obstacle were considered to affect research activities by most of the respondents, with 90% identifying financial obstacles. There were significant differences by gender, scientific rank, field of study, and holding executive responsibilities but not for durations of work experience. Despite these numerous obstacles to conducting research, respondents did not think their research output was affected.