Background: Chronic Rhinosinusitis (CRS) is characterized by inflammation of nose and paranasal cavities. High prevalence of respiratory viruses was detected in CRS patients. Objectives: To investigate prevalence of respiratory viruses in nasal mucosa of CRS patients and their association with allergic conditions. Methodology: The study included 30 CRS patients and 30 controls. Nasal wash samples were obtained from participants and nasopharyngeal swabs from 10 patients and controls, viral RNA extraction and multiplex nested PCR were performed to detect respiratory viruses. Results: Respiratory viruses were present in 53.3% of patients and 16.6% of controls (P= 0.003). Respiratory viruses were detected in 57.9% of allergic rhinitis and 50% of asthma patients. Comparing between sampling techniques showed that nasopharyngeal swabbing detected respiratory viruses in 70% of cases and 50% of controls, while nasal wash samples revealed viruses in 30% of patients and 10% of controls. Rhinovirus (RV) was the most commonly detected virus. Conclusions: Respiratory viruses are prevalent with CRS. The co-presence of CRS with AR and/or asthma suggests their relationship to disease progression. Multiplex nested PCR facilitated rapid and sensitive virus detection.