Functional gastrointestinal disorders (FGIDs) are common worldwide and cause considerable social and economic burden. The aims of SEPAHAN project were to 1) assess the prevalence of different FGIDs within an Iranian population, 2) investigate the relationship of FGIDs and their symptoms with lifestyle and nutritional factors, and 3) investigate the relationship of FGIDs and their symptoms with psychological factors. It was a cross-sectional study among staff of Isfahan University of Medical Sciences and Health Sciences (Isfahan, Iran) and consisted of two main phases. In the first phase, a detailed dietary questionnaire was used to assess dietary habits and usual dietary intakes. Other lifestyle factors were investigated using appropriate questionnaires. In the second phase, the epidemiology of different FGIDs was determined using Rome III criteria. In addition, different psychological assessment tools were used to screen for anxiety, depression, psychological distress, coping styles, stressful life events, personality trait, and level of social support. Self-administered questionnaires were used in this study. In the first and second phases of the study, 8691 and 6239 adults were recruited, respectively. The complete information of 4763 subjects has been provided after linking the questionnaires from both phases. SEPAHAN project is a novel study that provides the opportunity of investigating epidemiological aspects of FGIDs and their relationship with different lifestyle and psychological factors.