Bifidobacterium longum (BL999), Lactobacillus rhamonosus (LPR), prebiotics (inulin and fructo-oligosaccharides), and long-chain polyunsaturated fatty acids (LCPUFA) are believed to have health benefits. In a randomized, double-blind, controlled trial we compared growth and development of toddlers fed milk containing synbiotics (BL999, LPR, and prebiotics) and LCPUFA or a control milk. Three hundred and ninety three healthy, 12 month-old toddlers were fed approximately 400 mL/day for 12 months. Anthropometric measurements were taken at 12, 14, and 16 months. Toddlers' response to measles and hepatitis A vaccine was measured at 16 months, and Bayley scale for motor, cognitive, and behavioral functions made at 24 months. The primary outcome was weight gain between 12 and 16 months. Secondary outcomes were gain in length, head circumference, and body mass index, gastrointestinal tolerance (stool characteristics), stool bacterial counts, safety, anti-vaccine IgG, and neurodevelopment. Weight gain was greater in the synbiotics group (mean±SD, 7.57±4.13 g/day) compared with the control group (6.64±4.08 g/day). The difference of 0.93 g/day (with a 95% confidence interval of 0.12 to 1.75) is significant (p=0.025). The gain in the synbiotics group resulted in a change in z-score weight-for-age closer to WHO Child Growth Standard. There was a significant increase in lactobacilli and enterococci counts between 12 months and 16 months in the synbiotic group. We conclude that in healthy toddlers milk containing synbiotics and LCPUFA provides better growth and promotes favorable gut colonization, as shown by higher Lactobacillus counts.