Most paranasal sinus mucoceles are unilateral and affect one or at most two contiguous sinuses. We describe the case of a 44-year-old woman with bilateral maxillary sinus mucoceles who presented clinically with left malar pain, right-sided swelling, and proptosis of the right eye. The diagnostic workup included computed tomography and magnetic resonance imaging. In addition, because of the atypical bilateral presentation, we analyzed mucosal sinonasal tissue samples by electron microscopy. Microscopic analysis revealed an absence of one of the microtubule doublets in three of the outer doublets of the axoneme, thereby establishing a diagnosis of isolated ciliary dysfunction. To the best of our knowledge, ciliary dysfunction as a cause of bilateral mucoceles has not been previously reported in the literature. The patient underwent successful surgery for removal of the mucoceles, and she exhibited no evidence of recurrence at the 18-month follow-up. When a diagnosis of bilateral mucocele formation is made, we suggest that ciliary dysfunction be considered in the differential diagnosis and that electron microscopy of the sinonasal mucosa be performed in the workup.