Though mucosal cysts in the paranasal sinuses (PSMCs) are common findings on radiographic images, the nature of PSMCs and risk factors for the development of PSMCs have not yet been determined. The aim of this study was to evaluate the characteristics of PSMCs using brain magnetic resonance (MR) imaging. A total of 6831 subjects who underwent health checkup including brain MR imaging were included in this study. The characteristics of PSMCs, including their location, number and size, as well as the presence of obstruction of the sinus ostium and sinusitis, were analysed using brain MR images. Structured questionnaires and medical records were reviewed to evaluate the smoking status and comorbid medical conditions. The overall prevalence of PSMCs was 7.4% and was significantly higher in females than in males. PSMCs were most commonly found in the maxillary sinus, most of which were located unilaterally as a solitary cyst. Large cysts were associated with obstruction of the sinus ostium and subsequent sinusitis. Smoking was a single important risk factor for developing PSMCs. No significant associations were found between symptoms (nasal/respiratory) and the presence of PSMCs. The prevalence of PSMCs was 7.4% and decreased with age. Large cysts may lead to obstruction of the sinus and subsequent sinusitis. Smoking was an important risk factor for PSMCs, and the total amount of smoking correlated with cyst size. Most subjects were asymptomatic, and specific treatment was not performed.