Human stool-based products composed of fecal microbiota are a new frontier of medical therapeutics development. The development of standardized manufacturing protocols of donor microbiota has transformed fecal microbiota transplantation (FMT) from a crude and rarely used procedure to a widely accepted and highly effective option for treatment infections. There is also a growing interest in using microbiota transplant therapies for multiple other clinical indications. In this manuscript, we review the logistical challenges experienced by various stool banks and our own group in establishing and administering a stool donor program. Furthermore, we explore and highlight the multiple ethical considerations that are ultimately essential to product safety and efficacy and propose basic principles that are necessary to maintain stool donor program integrity.