Background: Physiological and pathological skin eruptions are commonly encountered in neonates in our clinical practice. However, the types of skin eruptions that are associated with the subsequent development of atopic dermatitis and the mechanisms of these associations remain uncertain. Methods: A total of 105 newborn babies with normal delivery were enrolled in this prospective cohort study. The cord blood eosinophil count was measured and the neonates were examined at 1 month of age and followed until 8 years of age. Results: At 1 month of age, infantile eczema, seborrheic dermatitis, intertrigo and diaper dermatitis were diagnosed in a total of 29, 7, 14 and 24 neonates, respectively. No association was found among the prevalences of these eruptions. Neonates with infantile eczema had a significantly higher number and ratio of eosinophils in the cord blood (eosinophil count: 670.8 ± 67.8 vs. 349.0 ± 30.3/µl, p < 0.0001; eosinophil ratio: 5.12 ± 0.53 vs. 2.61 ± 0.22%, p < 0.0001, for the presence and the absence of infantile eczema, respectively). In contrast, no such tendency was found for any other skin eruptions. In neonates with infantile eczema at 1 month of age, the diagnosis of atopic dermatitis had been made significantly earlier and the prevalence of wheezing illness was significantly higher than in those without infantile eczema until 2 years of age. Conclusion: Infantile eczema, but not other skin eruptions, precedes the development of atopic dermatitis and wheezing illness during early infancy, presumably because of the activation of eosinophils before birth.