A total diet study (TDS) was conducted in France to assess the health risks related to the chemicals in food of non-breastfed children under three years of age (Infant TDS). For the first time, substances coming from food contact materials, such as bisphenol A (BPA), bisphenol A diglycidyl ether (BADGE) and its derivatives, some phthalates, and some ink photoinitiators, were targeted because of growing interest in these substances. Food samples were collected to be representative of the whole diet of non-breastfed children aged 1–36 months, and prepared as consumed prior to analysis. Dietary exposure was assessed for 705 representative children under three years of age. Generally, the substances from food contact materials were detected in few samples: 38% for BPA, 0% for BADGE and its derivatives, 0–35% for phthalates, 1.9% for benzophenone, and 0% for the other ink photoinitiators. Regarding exposure levels, the situation was deemed tolerable for BADGE and its hydrolysis products, di-isodecyl phthalate, dibutyl phthalate, butyl benzyl phthalate, bis(2-ethylhexyl) phthalate, and di-isononyl phthalate, benzophenone, and 4-methylbenzophenone. Only for BPA, the exposure levels of some children exceeded the lowest toxicological value established by the French Agency for Food, Environmental and Occupational Health & Safety at 0.083 µg.kg bw−1.d−1. The temporary tolerable daily intake of the European Food Safety Authority (EFSA), set at 4 µg.kg bw−1.d−1, was never exceeded. However, actual exposure to BPA was probably overestimated, as well as the associated risk, because the foods were sampled prior to the recent regulations banning BPA in food packaging. This study is the first worldwide to provide an estimate of infant food contamination levels and exposures of children under 3 years of age, based on a TDS approach. It therefore provides key data on the exposure of this particularly sensitive population to substances released from food contact materials, and presents useful data for studies evaluating exposure to mixtures or aggregated exposure.