Objective: The stability and composition of intestinal flora plays a vital role in human wellbeing throughout life from as early as birth. Over the past 50 years, several studies have been conducted to evaluate the effect of probiotic administration in pediatric gastroenterology. This document aims to provide a recommendation score on probiotic utilization in pediatric gastroenterology, together with a review of current knowledge concerning its benefits, tolerability, and safety. Study Design: Published literature was selected without study design restriction: clinical guidelines, meta-analyses, randomized controlled trials (RCTs), cohort studies, outcomes research and case–controlled studies were selected using the following MESH-validated terms: probiotics, diarrhea, acute diarrhea, antibiotic-associated diarrhea, traveler’s diarrhea, bacterial diarrhea, nosocomial diarrhea, prophylactic diarrhea, Helicobacter pylori infection, colic, infantile colic, necrotizing enterocolitis (NEC), inflammatory bowel disease, constipation, and allergy. Once the validity and the quality of results were evaluated, a recommendation score and level of evidence were assigned for pediatric gastrointestinal-related conditions, according to the updated Evidence-Based Medicine guidelines: 1a for systematic review (SR) of RCTs, 1b for individual RCT, 1c for SR and individual RCT, 2a for SR of cohort studies, 2b for individual cohort studies, 2c for outcomes research, and 3a for SR of case-control studies. Results and Conclusions: The Latin American Expert group consensus recommends the use of the following probiotics for pediatric gastrointestinal conditions: prevention of acute infectious diarrhea (AID): 1b for Bifidobacterium lactis, Lactobacillus rhamnosus GG (LGG), and L. reuteri; prevention of nosocomial diarrhea: 1 b for B. lactis Bb12, B. bifidum, LGG and Streptococcus thermophiles; treatment of AID: 1a for LGG and S. boulardii, 1b for L. reuteri; prevention of antibiotic-associated diarrhea: 1b for LGG and S. boulardii; prevention of traveler’s diarrhea: 1b for S. boulardii; prevention of infantile colic: 1a for L. reuteri DSM 17938; treatment of infantile colic: 1b for L. reuteri DSM 17938; prevention of NEC: 1a for B. breve, mixtures of Bifidobacterium and Streptococcus, LGG, L. acidophilus and L. reuteri DSM 17938; induction and maintenance of remission in ulcerative colitis: 1b for VSL#3; improving symptoms of irritable bowel syndrome: 2c for LGG and VSL#3.