The inorganic selenium compounds selenite and selenate are used for selenium fortification of infant formulas. However, information on absorption and retention of selenium from these compounds is lacking. The purpose of this study was therefore to determine apparent absorption and retention of selenium from selenate and selenite added to a milk-based infant formula in healthy infants. Labeled test meals were prepared by addition of 10 μg Se as 76Se-selenate or 74Se-selenite to 500 mL formula. The two batches of labeled formulas were fed as alternate feeds during the first day of the balance period, followed by unlabeled formula. Selenium isotopes were determined in feces collected for 72h after intake and in 3 consecutive 24h collections of urine. Mean apparent absorption was 97.1% for 76Se-selenate and 73.4% for 74Se-selenite; mean difference 23.7% (range: 13.8%35.7%; SD 6.8%, p < 0.001). Mean urinary excretion (% of ingested dose) was 36.4% (76Se-selenate) and 9.7% (74Seselenite); mean difference 26.7% (range: 13.9%-36.5%; SD 5.9%, p < 0.001). Mean apparent retention of selenium from 76Se-selenate and 74Se-selenite was not significantly different, 60.7% (76Se-selenate) versus 63.7% (for 74Se-selenite). The average difference was -3.01% (range: -14.0%-12.0%; SD 9.4%, p = 0.36). Although apparent selenium absorption and urinary excretion differed for selenite and selenate, selenium was equally well retained by infants from both selenium compounds. We therefore concluded that Se fortification of infant formulas with selenate or selenite can be expected to have similar impact on the selenium nutritional status of term infants.