During the first few years of life the diversity of the gut microbiome increases with increasing age. Many factors influence the colonisation after birth and during infancy. There are some studies that have looked at the use of probiotics as a treatment for gastrointestinal distresses in children with some success. These studies however focus on the outcome. They do not consider the differences in gut microbiota in children and do not look at individual responses to probiotics. The purpose of this randomized, double-blinded, placebo-controlled trial was to understand the effect of a probiotic treatment on children under 4 years old admitted to the emergency department of hospital with acute diarrhea. 70 children were included (30 in the probiotic group, 32 placebo). Stool analyses were done on admission (day 0), then 5 days after administration of a probiotic or placebo and then again at day 28. The results showed that participants younger than 1 year had lower bacterial diversity than older children. The age of the child is a dominant factor in determining the overall diversity of the gut microbiome. Probiotic treatment for 5 days did not alter the composition of the gut microbiota. However, there was lower diversity in the presence of enteric bacterial pathogens; in particular, with C. difficile in stool samples. This study highlights that base line measurements should be included and that age is a key factor when designing future studies of this kind.