Significant bleeding during functional endoscopic naso-sinusal surgery (FESS) impairs recognition of anatomical references and may negatively affect surgical outcome. Through their hypotensive effect, adjuvant anaesthetic agents may influence intraoperative bleeding. The present study compared intraoperative bleeding in patients undergoing FESS administered a clonidine-based anaesthetic regimen and in patients receiving other an anaesthetic combination with higher acquisition costs. Prospective observational study included 37 subjects undergoing FESS in 2011. Assessment of intraoperative bleeding was according to type of anaesthesia (clonidine vs. opioid derivatives). Patients receiving clonidine (N = 11; 29.7%) presented significantly lower surgical field bleeding scores than those receiving opioid derivatives (N = 26; 70.3%) [mean (SD) Boezaart scores 1.91 (0.53) vs. 2.92 (0.79), p < 0.0001]. The multivariate analysis including baseline characteristics and risk factors related to bleeding intensity showed that the type of drug used for controlled hypotensive anaesthesia was the best predictor of bleeding during FESS, with an OR of 0.03 for clonidine based vs. opioid based anaesthesia (p = 0.014). The anaesthetic combination including clonidine for controlled hypotensive anaesthesia produces lower levels of surgical field bleeding during FESS. Compared with other hypotensive anaesthetics, clonidine is inexpensive and associated with better surgical conditions during FESS. If confirmed through randomized clinical trials, the use of clonidine during FESS can reduce surgical time and improve surgical results through a less bloody field, resulting in lower patient morbidity and improvement of operating room resources.