Hypoxia is most often caused by an underlying illness that affects blood flow or breathing. Conditions that can lead to hypoxia include: Anemia. Asthma. Bronchitis. Chronic obstructive pulmonary disease (COPD). Congenital heart defects. Congestive heart failure. Emphysema. Pneumonia (bacterial and viral). Pneumothorax (air in the space around the lung or collapsed lung). Pulmonary edema (fluid on the lungs). Pulmonary embolism (blood clot in the lung). Pulmonary hypertension. Pulmonary fibrosis (lung scarring). Sleep apnea.