Inflammation and endothelial dysfunction are key components in atherogenesis. Should the status of these pro-atherogenesis factors be enhanced during prolonged confined space travel, specific countermeasures need to be instituted to prevent these processes to ensure safe outcome for astronauts during space expeditions. Six crew members were exposed to prolonged, confined isolation for 520 days. Standard exercise and diet regime were instituted throughout isolation phase. Age and gender-matched healthy, free living controls were recruited in parallel. Serial serum and whole blood were analysed for biomarkers of inflammation (hsCRP and IL-6) and endothelial activation (sICAM-1, sVCAM-1 and E-selectin). Flow-mediated dilatation (FMD) of the artery was performed following the standard protocols set by the International Brachial Artery Reactivity Task Force by trained personnel. There was decreased sVCAM-1 concentration in crew members compared to baseline. However, there was significant decrease in percentage dilatation from baseline in FMD of the brachial artery in the crew members. Percent change increment was observed in hsCRP while percent change reduction was seen in sVCAM-1. The enhanced inflammation and reduced endothelial function could possibly be attributed to the rigorous exercise instituted throughout the confinement period. Furthermore, possible haemoconcentration as a result of psychosocial stress and/ or exercise-induced physiological response could further explain elevations in hsCRP, and unlikely pathological. Furthermore, endothelial activation was attenuated during isolation, suggesting that the diet and exercise program instated throughout the period improved endothelial function.