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Abstract Background Isolated right upper lobe pulmonary agenesis is a highly uncommon congenital anomaly, usually detected at adulthood when the patient is evaluated for an incidental abnormal chest radiograph. Chest radiography findings are non-specific. Chest computed tomography with pulmonary angiography is the modality of choice for diagnosing pulmonary agenesis. Case presentation We describe a case of isolated right upper lobe agenesis in a young man who presented with mild shortness of breath and an abnormal chest radiograph. High-resolution computed tomography chest showed right upper lobe pulmonary agenesis which was initially erroneously diagnosed as right lower lobe collapse on chest X-ray. Abnormal segmentation of the middle lobe was also seen which has not been described earlier according to our literature search. Conclusions There should be a high index of suspicion for congenital anomalies on chest X-ray to recommend further imaging studies. This case highlights the importance of computed tomography with pulmonary angiography to adequately assess and characterize the congenital lung anomalies.