During their processing, the infant formulas (IFs) are subjected to different thermal processes, which affect their safety and nutritional value, being influenced by the quality and type of ingredients used. The objective of this study was to evaluate the effect of ingredients used in commercial powdered IFs on furosine, HMF, furfural, available lysine content and evaluation of possible toxic effect of furanic compounds. Principal components (PC) and cluster analysis (CA) were employed to investigate relationships among IFs and indicators. Two PC were obtained which explain 77.3% of the total variance, grouping the IFs in five clusters. Significant higher values of available lysine were obtained in IFs with whey milk or skimmed milk; likewise, furosine was obtained in IFs with lactose, whey milk, milk proteins, skimmed milk or partially hydrolyzed whey (PHW). Significant higher values of HMF and furfural were obtained in IFs with starch. The maximum free furanic compounds provided by IFs were of 1.7 mg/person/day. HMF content does not represent a risk to the babies’ health. All IFs except one cover more than 90% of available lysine needs for a 3-month aged baby. PC and CA are useful to evaluate heat damage in IFs.