Background <p>Human milk palmitic acid (PA) is mainly esterified at the sn-2 position of triacylglycerols, while infant formula contains palmitate predominantly in the sn-1/3 positions. Current evidence on long-term health effects of increasing sn-2 palmitate in formula remains insufficient. This study investigated the effects of high sn-2 PA formula (&gt; 40%) on fecal saponified fatty acid, calcium, magnesium and stool characteristics in healthy full-term infants.</p> Methods <p>In this cluster-randomized controlled trial, healthy infants &lt; 14 d were assigned to breastfeeding (BF group, <i>n</i> = 66), high sn-2 palmitate formula (sn-2 group, <i>n</i> = 66, 46.3% sn-2 PA) or low sn-2 palmitate formula (control group, <i>n</i> = 67, 10.3% sn-2 PA). Infant demographics, feeding status, stool characteristics, physical exams, and stool samples were collected at 6, 16, and 24 weeks. Per-protocol analysis was used.</p> Results <p>The sn-2 group exhibited a significant time-dependent decline in fecal saponified PA and calcium over time (<i>P</i>_{<i>h for Trend</i>} &lt; 0.001). The BF group declined faster than the sn-2 group (<i>P</i>_{<i>adjusted for Group*Time</i>} &lt; 0.001). Fecal saponified PA proportion in sn-2 group was significantly lower than controls at all timepoints. At week 24, fecal calcium was lower in the sn-2 group vs. control (0.9 vs. 1.3&#xa0;mg/g, <i>P</i> = 0.010). No significant difference was found in stool frequency, consistency or size between sn-2 and control groups at any point.</p> Conclusion <p>Infant formula enriched with &gt; 40% sn-2 palmitate reduces fecal fatty acid and calcium excretion, supports efficient lipid and calcium absorption, shows a fecal magnesium pattern similar to breastfed infants, but does not alter stool characteristics relative to the control formula.</p> Trial registration <p>The trial is registered at Chinese Clinical Trial Registry: ChiCTR1800014479; 30/Jan./2018.</p>