Since 2014, several infections with non-tuberculous mycobacteria (NTM) belonging to the species Mycobacterium ( M.) chimaera have been associated with the use of heater-cooler devices during on-pump cardiothoracic surgery both in European countries and the United States of America. Infections have been detected after surgery, with a delay of a few months and up to five years. Bacterial contamination of heater-cooler devices has also been described without any associated infections. In many centres, it has been a challenging task to eliminate NTM from the heater-cooler devices in order to reduce the risk to patients. In this case-report, we describe how we managed to achieve negative cultures for M. chimaera by changing the cleaning procedure of the Sorin Group Heater-Cooler System with three tanks.