Minimally invasive endoscopic intracardiac surgery including one lung ventilation has been proposed to decrease surgical trauma but its impact on oxygenation and resource consumption has not been reported. We compared effects on gas exchange, induction, total anaesthesia time, staffing costs, and complications in 42 consecutive patients to a matched group undergoing similar surgery conventionally. Use of endoscopic compared to conventional surgery evoked a decrease in the PaO2/FIO2 ratio (mean (SD) 24.1 (14.9) vs 48.9 (14) kPa, p < 0.05) following termination of bypass with one lung ventilation (10 patients showed a PaO2/FiO2 below 13.3 kPa (100 mmHg)). There was also an increase of anaesthesia induction time (47 (13) vs 31 (9) min, p < 0.05), and an increase by 156 min of total anaesthesia time (474 (89) vs 321 (69) min, p < 0.05). Anaesthetist staffing costs increased by 300%. Thus, minimally invasive endoscopic intracardiac surgery consumes many more anaesthesia resources than conventional surgery and can result in hypoxaemia, but overall can be considered feasible provided that extensive continuous monitoring is employed.