Consumption of fructo-oligosaccharides (FOS) has been shown to improve mineral absorption in the short term, but no long-term effects were studied in girls with a low calcium intake. Therefore, we hypothesized that short- and long-term consumption of short-chain FOS (sc-FOS) improves calcium and magnesium absorption in girls with a low habitual calcium intake. Fourteen girls aged between 12 and 14 years received, for 36 days, 10 g sc-FOS (sc-FOS) or maltodextrin (placebo). Short-chain FOS were taken daily for 8 days followed by an intermittent intake mode on 28 random days to mimic noncontinuous intake. In a crossover design, true calcium and magnesium absorption was computed on the 8th and 36th day of each treatment period from isotope enrichment in urine. In addition, the parathyroid hormone and vitamin D in serum and markers of bone resorption in urine (pyridinoline and deoxypyridinoline) were determined. Short-chain FOS increased magnesium absorption by 18% after 36 days (30.1% ± 9.1% vs 35.4% ± 12.8%). Magnesium absorption did not change after the initial 8 days of long-term sc-FOS intake. Short-chain FOS did not affect calcium absorption. In addition, sc-FOS did not affect vitamin D, parathyroid hormone, or markers of bone resorption. It is concluded that consumption of sc-FOS for 36 days stimulated magnesium absorption in girls but did not affect calcium absorption. © 2009 Elsevier Inc. All rights reserved.