Allergies and bacterial colonization are frequently found in patients with chronic rhinosinuitis with nasal polyposis (CRSwNP). The aim of this study was to identify patients with allergy and present microorganisms in ethmoid sinus among the patients with refractory CRSwNP undergoing surgical treatment at the University Hospital Centre Osijek, and to compare their life quality, defined by SNOT-20 analysis (sinonasal outcome test) to the rest of patients, and a control group consisting of patients undergoing septoplasty but free of allergy and/or CRS. An additional aim was to identify specific types and strains of microorganisms (bacteria and fungi) found in these patients, in order to compare them to other reports, and to revise the empirical antimicrobial therapy. In this paper we demonstrate a high incidence of bacterial colonization (83.3%) among CRSwNP patients. As in previous studies, gram positive aerobes were the most frequently isolated bacteria and all of them were covered by specific antibiotics given before the specimen collection. Allergy was found in only 20% of these patients, who presented with a reduced quality of life when compared to the control group and CRSwNP without allergy. Significantly more frequent dominant symptoms in these patients were cough, frustration and irritation. In the line with this finding is the objective assessment by endoscopy (Malm score) that showed more prominent nasal polyposis in allergy patients.