The incidence of atopic dermatitis (AD) is increasing worldwide. Clinical studies have observed reduced risks of AD among infants fed with 100% whey partially hydrolyzed infant formula (PHF-W) compared with intact protein cow's milk formula. To evaluate this potential relationship more comprehensively, a systematic review of the literature was conducted. Studies (n = 18, representing 12 distinct study populations) that specified the protein source of the formula, evaluated healthy-term infants, compared the use of PHF-W with intact protein cow's milk formula, and reported results for AD were included. A critical assessment of the methodological quality of studies was conducted. In all studies, a reduced incidence of AD and/or atopic manifestations that included AD was observed. The cumulative incidence of AD was significantly lower among infants over at least 3 years of follow-up in the PHF-W group compared with the intact protein cow's milk group. Exclusive breastfeeding should be encouraged as the primary means to prevent atopic risk. However, when infants are not exclusively breastfed, PHF-W may be considered an effective measure to potentially reduce the risk of developing AD.