Septoplasty is one of the most frequent surgical procedures performed by head and neck surgeons. Despite surgical correction, some patients are not satisfied with their postoperative outcomes. Only a few papers report data on the long-term quality of life of patients after septoplasty, and none over 36 months. This follow up study on 68 surgical procedures aims to evaluate the differences between short term and long-term quality of life after septoplasty using a disease specific quality of life questionnaire, the NOSE, and a general health status questionnaire, the SF-36. We found a statistically significant decrease of the total long-term SF-36 scores, but we did not find changes of the NOSE scores compared with the short-term scores. These results indicated that patients perceived a worsening of their quality of life after more than 36 months following septoplasty, even in the absence of specific nasal symptoms. We could speculate that the preoperative general health performance was erroneously attributed to specific nasal symptoms, probably incorrectly emphasized or that patients did not correctly remember the preoperative clinical status. This research pointed out the importance of patients’ selection and of a thorough evaluation of their preoperative expectations before surgical planning.