Background and aim The association between body mass index (BMI) and functional gastrointestinal disorders (FGIDs) has been inconsistent. We aimed to explore the association of BMI with FGIDs in a primary care setting to provide more data in this area. Methods A cross-sectional study of consecutive Asian adults attending a primary healthcare setting was conducted. This study was conducted in 2 phases: The association between BMI and common FGIDs (functional diarrhea/FD, irritable bowel syndrome/IBS, functional diarrhea and functional constipation/FC) was studied initially. The influence of anxiety and depression on BMI and FGIDs was additionally explored in phase 2. Results A total of 1002 subjects (median age 32 years, 65.4% females, 90.7% Malay ethnicity, 73.2% higher than secondary level education) were recruited between August 2019 to January 2020. The majority of subjects were obese (39.2%), and had central obesity (51.7%), while 6.1% had metabolic syndrome. The prevalence of FD, IBS, functional diarrhea and FC were 7.5% (n = 75), 4.0% (n = 40), 1.2% (n = 12) and 10.5% (n = 105) respectively, based on the Rome III criteria. Among individual FGIDs, FD subjects had more underweight adults (BMI Conclusions FD, but not other FGIDs, is associated with being underweight. This association is independent of the presence of anxiety.