Carrying out exposure studies on children who are not toilet trained is challenging because of the difficulty of urine sampling. In this study, we optimized a protocol for urine collection from disposable diapers for the analysis of phthalate metabolites. The exposure of Swiss children (n = 113) between 6 months and 3 years of life to seven phthalates was assessed by gas chromatography–mass spectrometry measurements. The study showed limited exposures to phthalates, with only 22% of the samples containing some of the metabolites investigated. The three most frequently detected metabolites were monoethyl phthalate, mono-cyclohexyl phthalate, and mono-benzyl phthalate. We also detected mono-n-octyl phthalate and mono(3,5,5-trimethylhexyl) phthalate, which have rarely been observed in urine from infants and toddlers; therefore, di-n-octyl phthalate and bis(3,5,5-trimethylhexyl) phthalate can be considered as potentially new emerging phthalates. This study presents an initial snapshot of the Swiss children’s exposure to phthalates and provides a promising approach for further phthalate biomonitoring studies on young children using disposable diapers as urine sampling technique.