Background: Fecal microbiota transplant (FMT) is a treatment modality that involves the introduction of stool from a healthy pre-screened donor into the gastrointestinal tract of a patient. It exerts its therapeutic effects by remodeling the gut microbiota and treating microbial dysbiosis-imbalance. FMT is not regulated in Jordan, and demarcating regulatory framework for FMT therapy in Jordan, an Islamic conservative country, might be faced with unique cultural, social, religious and ethical challenges. The aim is to assess knowledge, attitudes and perceptions of ethical and social issues of FMT among Jordanian healthcare professionals.Methods: An observational, cross-sectional study design was used to assess knowledge, attitudes and perceptions of ethical and social issues of FMT among 300 Jordanian healthcare professionals. Results: A large proportion (39%) thought that the safety and efficacy of this technique is limited and 29.3% thought there is no evidence to support its use. Among the choices to select to use FMT, almost all (95%) would only perform it in certain cases, if ethically justified, and 48.3% would use it due to treatment failure. And for reasons not to use it, 40% would not perform it due to concerns about medical litigation, followed by fear of infections (38 %), and lack knowledge of long safety and efficacy (31.3 %). Interestingly, all practitioners would perform this procedure through the lower gastrointestinal tract modality and the majority will protect patient’s confidentiality via double-blinding (43.3%). For a subset of participants (n=100), the cultural constrains that might affect the choice of performing FMT were to the donor's religion, and dietary intake and alcohol consumption.Conclusion: Our health care practitioners are reluctant to use the FMT modality due to religious and ethical reasons but would consider it if there was failure of other treatment and after taking into consideration many other social and ethical restrictions.