Conclusion: Staphylococcus aureus, Streptococcus, Haemophilus, Enterobacter, and Corynebacterium appear to be more frequently associated with patients with chronic rhinosinusitis (CRS) with nasal polyps (CRSwNP) than with patients with CRS without nasal polyps (CRSsNP) or control subjects. Furthermore, the isolation rate of Staphylococcus aureus appears to be much lower in Chinese CRSwNP patients compared with their caucasian counterparts. Objectives: To compare the predominant bacteriologic profiles in middle meatus of patients with CRSwNP, those with CRSsNP, and control subjects. Methods: A total of 165 CRSwNP patients, 76 CRSsNP patients, and 44 control subjects were recruited into the study. Swab samples were obtained from the middle meatus during endoscopic sinus surgery and processed for the presence of aerobic and non-aerobic bacteria and fungi. Results: Mostly aerobic and facultative anaerobic bacteria were detected in the samples from all three study groups, of which the most common aerobic bacteria were coagulase-negative staphylococci, Corynebacterium species, Staphylococcus aureus, and Haemophilus influenzae. In contrast, comparatively few anaerobic bacteria and fungi were isolated from the three study groups. In CRSwNP patients, significantly more Gram-negative aerobic and facultative anaerobic bacteria were isolated from the subgroup with normal eosinophil numbers than from the subgroup with increased blood eosinophils (p = 0.005). Correspondence analysis showed coagulase-negative staphylococci to be closely associated with all three patient groups, whereas Staphylococcus aureus, Streptococcus, Haemophilus, Enterobacter, and Corynebacterium species were associated with CRSwNP patients.