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Background Long-term non-invasive ventilation (LT-NIV) may reduce the number of exacerbations and prolong survival in patients with COPD. Atelectasis is frequently reported on chest CT scan in these patients; however, the prognostic impact of this finding is not fully understood. The aim of this project to investigate the prevalence on atelectasis in patients with COPD on LT-NIV and its clinical impact.Methods 347 patients with COPD participating in our prospective cohort who had a chest CT were studied.Results 239 patients (69%) had atelectasis reported on their chest CT scan. Atelectasis was not associated with the number of exacerbations before or after LT-NIV setup (all p>0.05). In contrast, the 5-year survival for patients with atelectasis was significantly lower compared to those who did not have atelectasis (50% vs. 65%, p<0.05). The overall mortality post-setup significantly related to the presence of left upper lobe atelectasis (n=98, p=0.03) and right middle lobe atelectasis (n=61, p=0.01) as well as the number of lobes affected by atelectasis (p=0.01).Conclusion Atelectasis on chest CT scan is associated with worse clinical outcomes and may represent a treatable trait (i.e. physiotherapy for secretion management) in patients with COPD.