The direct visualization of systemic microcirculation using intravitalmicroscopy permits the classification of proinflammatory and ischemic microvascular alterations during normothermic and hypothermic cardiopulmonary bypass in neonates. We used seven newborn piglets, on average aged 9 days, and weighing 3200 g, as a control group. In addition, we studied nine piglets subjected to 60 minutes of constant non-pulsatile flow using hypothermic extracorporeal circulation at 28°C, and five piglets using normothermic conditions at 37°C. The microvascular network of the greater omentum and the subcutaneous tissue was directly visualized using intravitalmicroscopy. We analysed interactions between leukocytes and endothelial cells, microvascular morphology, and microrheological conditions, focussing on signs of ischemic and proinflammatory alterations. During normothermic cardiopulmonary bypass, the numbers of activated leukocytes were elevated compared to hypothermic cardiopulmonary bypass (p > 0.05). Arteriolar diameter decreased during hypothermia. Capillaries were markedly dilated during normothermia. Patterns of microvascular perfusion, for both types of cardiopulmonary bypass, showed signs of ischemic damage, revealed by a reduced functional capillary density. Perfusion dependent levels of lactate were higher during normothermic cardiopulmonary bypass (p > 0.05). This new experimental approach revealed that non-pulsatile cardiopulmonary bypass, independent of temperature, induces a proinflammatory and ischemic response compared to an unaltered control group. The markedly elevated numbers of activated adherent leukocytes, the reduced capillary density, and the high lactate levels in those undergoing bypass in normothermic conditions indicate a more pronounced inflammatory stimulus and tissue hypoperfusion compared to the possible protective effect of hypothermia for children undergoing cardiopulmonary bypass.