Probiotics have gained worldwide use during the last two decades. However, which probiotic to use in which clinical condition has remained confusing in some clinical conditions. We convened a workshop at Yale in conjunction with Harvard in 2005, inviting a spectrum of probiotic authorities to discuss and reach conclusions on recommendations for use in common clinical conditions; the workshop was reconvened again in 2008 and in 2011. Each time the group of authorities was enlarged and varied depending on research studies. This article lists the recommendations updated from 2011 and is amended to bring it up to date in childhood and adult diarrhea, antibiotic-associated diarrhea, necrotizing enterocolitis, inflammatory bowel disorders, irritable bowel syndrome, allergic disorders, and radiation enteritis pending our 4th Triennial Yale/Harvard workshop to be convened in 2015.