Introduction and objective: Chronic rhinosinusitis is often diagnosed in the paediatric population. The pathogenesis of the condition is a complex and not fully understood process involving disorders of the immune system, allergies, and environmental and social aspects. The study aimed to determine the clinical, immunological, and microbiological factors influencing the clinical course of chronic rhinosinusitis in preschool and early school-age children. Materials and methods: This cross-sectional study included one hundred and eleven children aged 4–8 years, with chronic rhinosinusitis diagnosed by otolaryngologists. The following procedures were performed in each patient: a standardised SN-5 (Sinus and Nasal Quality of Life Survey) questionnaire, a questionnaire evaluating the applied treatment, skin prick tests with inhaled allergens, and nasopharyngeal swab for microbiome analysis. Results: The univariate regression analysis found that children who had previously attended nursery, children who were allergic to perennial allergens and house dust mites, and children with atopy, demonstrated more severe symptoms of chronic rhinosinusitis (SN-5 >3.6 pts). The multivariate model confirmed that the only independent factor for a more severe course of chronic rhinosinusitis (odds ratio, OR = 4.1; 95% confidence interval, 95% CI: 1.4–11.9; p = 0.007) was the children’s allergy to house dust mites. Conclusions: House dust mite allergy may increase the severity of chronic rhinosinusitis in young children, which justifies an attempt to implement additional recommendations for the treatment of allergic inflammation.