Sleep-disordered breathing (SDB) is a risk factor for cardiovascular disease (CVD). The underlying pathogenesis is not clear. In patients with obstructive sleep apnoea syndrome (OSAS) elevated levels of inflammatory markers, such as C-reactive protein (CRP), interleukin-6 (IL-6) and tumour necrosis factor α (TNFα) have been found. These markers have also been shown as independent markers of CVD in other populations. The aim of the study was to investigate the association between SDB and systemic inflammation in a population-based cohort of women. From 6817 women who previously answered a questionnaire concerning snoring habits, 230 habitually snoring women and 170 women regardless of snoring status went through polysomnography, anthropometric measurements and blood sampling. Analyses were made for CRP, TNFα, IL-6, myeloperoxidase (MPO) and lysozyme. The levels of CRP, IL-6 and lysozyme were significantly higher in subjects with apnoea-hypopnoea index (AHI) ≥15 compared with women with lower AHI. All inflammatory markers except MPO correlated to AHI and oxygen desaturation measures, and to waist circumference. In multiple linear regressions adjusting for age, waist circumference and smoking, independent correlations between oxygen desaturation indices (ODI) and inflammation were found for IL-6 (P = 0.03 for % sleep time with saturation <90%) and TNFα (P = 0.03 for ODI 3%). No significant correlations were found between AHI and inflammation. Also, for women from the general population there is an independent correlation between SDB and inflammation, even after adjusting for obesity. The results indicate that intermittent hypoxia, and not the AHI, is related to systemic inflammation seen in OSAS.