Background: Allergic rhinitis (AR) is the most common allergic disease in children and is closely associated with asthma in the context of atopic march. The development process of AR in early childhood, however, is not well understood due to the absence of definitive diagnostic criteria. We prospectively investigated the process in regard to not only the nasal symptoms and sensitization, but also the nasal cytology, in relation to asthma in a high-risk cohort. Methods: Infants under 2 years of age with atopic dermatitis (AD) and/or food allergy (FA) without a diagnosis of asthma were recruited and followed prospectively for 2 years. The phenotype of perennial AR was classified based on the presence/absence of 1) persistent nasal symptoms, 2) nasal eosinophils and 3) HDM sensitization, the most common allergen for perennial AR in Japan. AR-like phenotypes were defined as positive for at least 2 of those 3 categories. Results: A total of 304 children were enrolled, and 242 subjects (80%) completed the 2-year observation. The prevalence of eosinophilia in nasal secretions increased from 18.5% to 69.9%, while HDM-specific IgE >0.35 kUA/L increased from 30.6% to 74.8%. AR-like phenotypes increased from 18.4% to 65.0%. The cumulative incidence of physician-diagnosed asthma during the 2-year follow-up was significantly higher in the subjects with an AR-like phenotype at 1 year than in those with a non-AR phenotypes. Conclusions: The prevalence of an HDM-related AR-like phenotype was markedly increased during infancy in high-risk infants with AD/FA and was associated with asthma.