Several patients experience pulmonary sequelae after Sars-Cov-2 infection, ranging from self-limited abnormalities to major lung diseases. Morphological analysis of lung tissue may help in understanding pathogenic mechanisms and provide consistent personalised management. Aim of the study was to ascertain morphologic and immuno-molecular features of lung tissue. Transbronchial lung cryobiopsy was carried out in patients with persistent symptoms and computed tomography suggestive of residual lung disease after recovery from Sars-CoV-2 infection. 164 patients were referred for suspected pulmonary sequelae after COVID-19; 10 patients with parenchymal lung disease extent >5% underwent lung biopsy. Histological pattern was not homogeneous, as three different case clusters could be evidenced, which were mirrored in clinical and radiological features: cluster one (“chronic fibrosing”) characterised by post-infection progression of pre-existing interstitial pneumonias; cluster two (“acute/subacute injury”) characterised by different types and grades of lung injury, ranging from organising pneumonia and fibrosing NSIP to diffuse alveolar damage; cluster three (“vascular changes”) characterised by diffuse vascular increase, dilatation and distortion (capillaries and venules) within otherwise normal parenchyma. Clusters two and three were characterised by immunophenotypical changes similar to those observed in early/mild covid-19 pneumonias (abnormal expression of STAT3 in hyperplastic pneumocytes and PD-L1, IDO and STAT3 in endothelial cells). This is the first study correlating histological/immunohistochemical patterns with clinical and radiological pictures of patients with post-COVID lung disease. Different phenotypes with potential different underlying pathogenic mechanisms have been identified.