Infant formulas based on soyabean protein isolate are often used as an alternative to cows'-based formulas. However, the presence of phytic acid in soya formulas has raised concern about the absorption of trace elements and minerals from these products. The aim of the present study was to evaluate mineral and trace element absorption from regular and dephytinised soya formula in healthy infants. Soyabean protein isolate with a relatively low native content of phytic acid was used for production of a regular soya formula (300 mg phytic acid/kg liquid formula) and an experimental formula was based on dephytinised soya protein isolate (<6 mg phytic acid/kg liquid formula). Using a crossover study design, apparent mineral and trace element absorptions were measured by a stable isotope technique based on 72 h faecal excretion of non-absorbed stable isotopes (Zn, Fe, Cu and Ca) and by the chemical balance technique (Mn, Zn, Cu and Ca) in nine infants (69–191 d old). Fe absorption was also measured by erythrocyte incorporation 14 d after intake. The results from the present study demonstrated that Zn absorption, measured by a stable isotope technique, was significantly greater after dephytinisation (mean value 16·7 v. 22·6 %; P=0·03). No other statistically significant differences between the two formulas were observed. The nutritional benefit of dephytinisation was marginal in the present study. Based on these results, the use of soyabean protein isolate with low native content of phytic acid should be promoted for production of soya formulas and adequate addition of ascorbic acid to enhance Fe absorption should be ensured in the products.