Background Rhinologists are currently trying to find evidence useful for classifying chronic rhinosinusitis with nasal polyps (CRSwNP) in terms of pathophysiology-based endotypes. This would help us to tailor targeted therapies and follow-up protocols to each patient, improving treatment efficacy and reducing relapse risk. The histopathological study of inflammatory cells in tissue and their tendency to form aggregates has shown promise in determining the pathogenesis and predicting the clinical outcome. Objective The main purpose of this study was to assess tissue eosinophil count, eosinophil aggregation, and their relationship to different CRSwNP phenotypes. Methods A consecutive series of 96 patients who underwent endoscopic sinus surgery for CRSwNP was retrospectively assessed. Our structured histopathological approach considered eosinophil count and eosinophil aggregates. Results Patients’ clinical features included allergic fungal rhinosinusitis (AFRS) in 17 cases, nonsteroidal anti-inflammatory drug-exacerbated respiratory disease (NERD) in 19 cases, intrinsic asthma in 18 cases, extrinsic asthma in 21 cases, and allergy in 21 cases. Statistical analysis revealed more eosinophil aggregates in patients with NERD than in those with AFRS ( P = .020), intrinsic asthma ( P = .019), or extrinsic asthma ( P = .029). NERD patients had a significantly higher tissue eosinophil count than the other groups considered, apart from the AFRS ones. AFRS patients had a higher tissue eosinophil count than patients with intrinsic asthma. Conclusion Our results showed in particular that the NERD patient group’s rhinosinusitis was sustained by a significantly more severe eosinophilic reaction than in the other groups. Structured histopathology can provide useful information for classifying CRSwNP on pathophysiological grounds.