Yacon roots have been considered a functional food due to the high levels of fructans they contains. In the present study, Ca and Mg balance, bone mass and strength, and caecum mucosal morphometry were evaluated. Growing male Wistar rats (n 24) were fed ad libitum control diets or diets supplemented with yacon flour (5 or 7·5 % fructooligosaccharides) for 27 d. Mineral balance was evaluated in three periods of 5 d (starting on the 4th, 10th and 16th days). After the rats were killled, the bones were removed and bone mineral density was measured. Ca analyses were performed on left femurs and tibias and biomechanical testing on right femurs. The caecum was removed and tissue samples were collected for histological analysis. Caecal histology changed noticeably in rats fed yacon flour: there was an increase in the depth and number of total and bifurcated crypts as well. Yacon flour consumption significantly (P < 0·05) resulted in a positive Ca and Mg balance, leading to higher values of bone mineral retention and biomechanical properties (peak load and stiffness) when compared to the control group. The positive effects on mineral intestinal absorption, bone mass and biomechanical properties showed an important role of yacon roots in the maintenance of healthy bones. The increased number of bifurcating crypts might be related to the higher mineral absorption caused by the enlargement of the absorbing surface in the large intestine of the animals.