Background: Endoscopic sinus surgery (ESS) is considered after medical therapy failure of chronic rhinosinusitis (CRS). The balloon sinuplasty dilates the natural ostium without moving mucosa or bone. It still lacks evidence from randomized controlled trials. The aim of this retrospective controlled study was to compare the symptom outcomes after maxillary sinus surgery with either the ESS or the balloon sinuplasty technique. No previous or additional sinonasal operations were accepted.Methods: Two hundred eight patients with CRS without nasal polyps underwent either balloon sinuplasty or ESS. The patients who met with the inclusion criteria (n = 45 in ESS group and n = 40 in balloon group) replied to a questionnaire of history factors, exacerbations, and a visual analog scale (VAS) scoring of the change in symptoms, on average 28 ± 6 (mean ± SD) months postoperatively.Results: The groups were identical in the response rate (64%), patient characteristics, and the improvement in all of the asked symptoms. Patients with CRS-related comorbidity and/or present occupational exposure had a statistically significantly better symptom reduction after ESS than after balloon sinusotomy. Moreover, the balloon sinusotomy group reported a statistically significant higher number of maxillary sinus punctures and antibiotic courses during the last 12 months.Conclusion: ESS might be superior to balloon sinuplasty, especially in patients with risk factors. There is a need to perform more controlled studies on the treatment choices of CRS.