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Background The relationship between allergies and sinusitis, though extensively studied, remains poorly defined. While several studies proposed a cause-and-effect relationship between allergy and chronic sinusitis, several others reported the lack of any existing association. This study aimed to investigate the relationship between allergy and sinusitis. Methods We conducted a cross-sectional study using a representative sample of the US population from the National Health and Nutrition Examination Survey 2005‒2006 (n  = 7244). A self-reported allergy questionnaire and total and allergen-specific IgE levels were used for analysis. Participants were divided into positive and negative allergy symptoms groups (PAS, NAS, respectively) to eliminate the influence of allergy symptoms on the apparent incidence of sinusitis. Pearson’s chi-square test and the linear regression analysis using Durbin Watson test were used for statistical analysis. Results Sinusitis incidence in the PAS group (22.4%; 521/2327) was significantly higher than that in the NAS group (7.1%; 348/4917) [odds ratios (OR)  = 3.788, 95% confidence interval (CI) 3.272‒4.384, P  < 0.001]. sinusitis incidence in non-sensitized and sensitized groups was not statistically different. After controlling for allergy symptoms, there was a negative correlation between sensitization status and the occurrence of sinusitis in the PAS group (OR  = 1.407, 95% CI 1.156‒1.711, P  < 0.01). Increase in serum total IgE levels correlated with decrease in incidence of sinusitis in both PAS and NAS groups. sinusitis incidence was significantly reduced in the PAS group in participants sensitized to allergens such as cockroaches, ragweed, ryegrass, Bermuda grass, oak, birch, and thistle. Conclusion Allergy is related to sinusitis incidence. It is likely that sensitization status could reduce the incidence of sinusitis, albeit in an antigen-specific manner.