Healthy 9- to 48-month-old children (n = 133) were randomized to receive a cow's-milk-based follow-on formula (control) or the same formula with polydextrose and galactooligosaccharides (PDX/GOS) for 108 days. Pediatricians assessed diarrheal disease, stool pattern, acute respiratory infection, systemic antibiotic use, and growth. The 2 groups had similar weight-for-length/height z score and similar odds of having diarrheal disease, acute respiratory infection, and systemic antibiotic use; however, PDX/GOS had greater odds of increased defecation than control (P ≤ 0.01). Addition of PDX and GOS to a follow-on formula was well tolerated and induced a pattern of more frequent and softer stools in toddlers.