As the result of the digestion process, it is produced at gastrointestinal level interactions between proteins-minerals and minerals-minerals that might modify the bioavailability of the nutrients initially designed for an adequate nutrition in infant formulas. The aim of the present study is to compare the in vitro availability of some minerals and trace elements (calcium, phosphorus, magnesium, iron and zinc) in infant formulas of initiation elaborated with different protein sources: formulas based on cow milk protein (whey-casein) versus vegetal protein (soy-based infant formulas). Also, for evaluating the effects of the different mineral supplementation in the availability of minerals, it was used infant formulas from two different manufacturers. Milk-protein based infant formulas showed for both manufacturers higher dialysis percentage (%) of phosphorus and zinc than the soy-protein based formulas. The availability of iron in the soy formula of the manufacturer A lowered significantly (P < 0.05) respect to the whey-casein based formula (9.6 +/- 2.3 versus 4.6 +/- 0.8), but not respect to the whey-casein formula of manufacturer B (9.6 +/- 1.1 versus 9.0 +/- 0.7), which might be due to the lowest proportion of phytic acid in this last commercial formula. Dialysability of all the minerals analysed from soy-protein based formulas showed significant differences depending on the manufacturer. The purification processes of the soy protein have a high repercussion in the mineral availability of soy-based infant formulas. It could be more interesting to use soy proteins more purified, with low level of phytic acid, in the elaboration of soy infants formulas, than the supplementation them with high amounts of minerals.