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The objectives of this study were to determine the mycology of the middle meatus using an endoscopically guided brush sampling technique and polymerase chain reaction laboratory processing of nasal mucous; to compare the mycology of the middle meatus in patients with sinus disease with subjects without sinus disease; to compare the responses on two standardized quality-of-life survey forms between patients with and without sinusitis; and to determine whether the presence of fungi in the middle meatus correlates with responses on these data sets.The authors conducted a single-blind, prospective, cross-sectional study.Patients with sinus disease and a control group without sinus disease were enrolled in the study. A disease-specific, validated Sinonasal Outcomes Test survey (SNOT-20) was completed by the subjects and a generalized validated Medical Outcomes Short Form 36 Survey (SF-36) was also completed. An endoscopically guided brush sampling of nasal mucous was obtained from the middle meatus. Fungal specific quantitative polymerase chain reaction (QPCR) was performed on the obtained sample to identify one of 82 different species of fungus in the laboratory. Statistical analysis was used to categorize the recovered fungal DNA and to crossreference this information with the outcomes surveys.The fungal recovery rate in the study was 45.9% in patients with sinus disease and 45.9% in control subjects. Patients with chronic rhinosinusitis had a mean SNOT-20 score of 1.80 versus the control group mean score of 0.77 (P < .0001). SF-36 data similarly showed a statistically significant difference between diseased and control populations with controls scoring a mean of 80.37 and patients with chronic rhinosinusitis scoring a mean of 69.35 for a P value of .02. However, no statistical significance could be ascribed to the presence or absence of fungi recovered, the type of fungi recovered, or the possible impact of fungi on the quality-of-life survey results.The recovery rate of fungi from the middle meatus of patients with chronic rhinosinusitis and a control population without chronic rhinosinusitis is 45.9% using QPCR techniques. No direct causation with regard to fungal species or presence was proven; however, a species grouping for future studies is proposed based on trends in this data and other reports. Disease-specific outcomes surveys revealed a statistically significant difference between the two groups.