We studied the spatial distribution of the abnormal V_A/Q units in a porcine model of acute pulmonary thromboembolism (APTE), using the fluorescent microsphere (FMS) technique. Four piglets (~22 Kg) were anaesthetized and ventilated with room air in the prone position. Each received about 20 grams pre-formed blood clots at time = 0 minutes via a large bore central venous catheter, until the mean pulmonary artery pressure reached 2.5 times baseline. The distributions of regional ventilation (V_A) and blood flow (Q) at five time points (t = -30, -5, 30, 60, 120 min) were mapped by FMS of 10 distinct colors, i.e. aerosolization of 1 µm FMS for labelling ventilation and intravenous injection of 15 µm FMS for labelling perfusion. Our results showed that at time = 30 minutes following APTE, mean V_A/Q (V_A/Q = 2.48 ± 1.12) and V_A/Q heterogeneity (Log SD V_A/Q = 1.76 ± 0.23) were significantly increased. There were also significant increases in physiological dead space (11.2 ± 12.7 % at 60 min) but the shunt fraction (V_A/Q = 0) remained minimal. Cluster analyses showed that the low V_A/Q units were mainly seen in the least embolized regions, whereas the high V_A/Q units and dead space were found in the peripheral subpleural regions distal to the clots. At 60 and 120 minutes, there were modest recoveries in the hemodynamics and gas exchange towards baseline. Redistribution pattern was mostly seen in regional Q while V_A remained relatively unchanged. We concluded that the hypoxemia seen after APTE could be explained by the mechanical diversion of blood flow to the less embolized regions because of the vascular obstruction by clots elsewhere. These low V_A/Q units created by high flow, rather than low ventilation, accounted for most of the resultant hypoxemia.