Nasal cytology at birth and in the pediatric age is barely investigated regarding its association with the onset of common pediatric diseases. We enrolled 241 newborns within their first 24 h of life, studying their nasal cellular composition and repeating this at 1 and 3 years of life. We collected anamneses of perinatal factors and external factors (parental smoking, passive smoking, breastfeeding), and the prevalence of otitis, rhinosinusitis, bronchitis, asthma, and allergy at all timepoints. 204 children completed the study. At birth, there was a prevalence of ciliated cells and rare neutrophils. At 1 and 3 years, ciliated cells started reducing in favor of muciparous cells and neutrophils. We found that caesarian delivery and nasogastric tube usage for choanal patency are significantly related to a certain cellular nasal composition. Additionally, development of upper respiratory tract infections, AOM (acute otitis media) and allergy correlates with specific cytological compositions which may predict those pathologies. Our study is the first to show the normal nasal mucosa cellular composition and development in the first 3 years of life in a large cohort. Nasal cytology may be a tool for early risk assessment in the occurrence of upper airway disease.