Soya-based infant formulas (SIF) containing soya flour were introduced almost 100 years ago. Modern soya formulas are used in allergy/intolerance to cows' milk-based formulas (CMF), post-infectious diarrhoea, lactose intolerance and galactosaemia, as a vegan human milk (HM) substitute, etc. The safety of SIF is still debated. In the present study, we reviewed the safety of SIF in relation to anthropometric growth, bone health (bone mineral content), immunity, cognition, and reproductive and endocrine functions. The present review includes cross-sectional, case–control, cohort studies or clinical trials that were carried out in children fed SIF compared with those fed other types of infant formulas and that measured safety. The databases that were searched included PubMed (1909 to July 2013), Embase (1988 to May 2013), LILACS (1990 to May 2011), ARTEMISA (13th edition, December 2012), Cochrane controlled trials register, Bandolier and DARE using the Cochrane methodology. Wherever possible, a meta-analysis was carried out. We found that the anthropometric patterns of children fed SIF were similar to those of children fed CMF or HM. Despite the high levels of phytates and aluminium in SIF, Hb, serum protein, Zn and Ca concentrations and bone mineral content were found to be similar to those of children fed CMF or HM. We also found the levels of genistein and daidzein to be higher in children fed SIF; however, we did not find strong evidence of a negative effect on reproductive and endocrine functions. Immune measurements and neurocognitive parameters were similar in all the feeding groups. In conclusion, modern SIF are evidence-based safety options to feed children requiring them. The patterns of growth, bone health and metabolic, reproductive, endocrine, immune and neurological functions are similar to those observed in children fed CMF or HM.