Infant foods and formulae may contain toxic substances and elements which can be neo-formed contaminants or derived from raw materials or processing. The content of minerals, toxic elements, and hydroxymethylfurfural (HMF) in infant foods and formulae were evaluated. The effect of storage temperature on HMF formation in infant formulae and its potential as a quality parameter was also evaluated. Prune-based foods contained the highest HMF content. HMF significantly increased when the storage temperature was elevated to 30 °C for 21 days. All trace elements were present in adequate amounts, while the concentration of nickel was higher when compared to those of other studies. The study indicates that HMF can be used as a quality indicator for product shelf-life and that the concentrations of minerals and toxic elements vary greatly due to the diverse compositions of foods and formulae. Such contaminants need to be monitored as infants represent a vulnerable group compared to adults.