When heat pipes are applied in atmospheres containing hydrogen, e.g. in presence of syngas, a small amount of hydrogen permeates through the wall of the containment into the heat pipe and accumulates as non-condensable at the end of the condenser. If the hydrogen is not removed during operation, this mechanism causes a rapid deactivation of the heat pipe starting from the condensation zone. This paper demonstrates the impacts of this deactivation on heat pipe operation and heat transfer rates and presents a formal description of the mechanism. Possible countermeasures to avoid this problem are presented and will be discussed, in particular the choice of safe operation conditions and the use of hydrogen windows based on metal membranes. The hydrogen deactivation was investigated both experimentally and theoretically. We will focus on the kinetics of the inactivation process as well as the equilibrium state when applying hydrogen windows for hydrogen removal. The results will be discussed in comparison with modelling approaches. The deactivation time from beginning of hydrogen sweep to complete inactivation of the heat pipe is in the range of 1-3 h. In the experiments a nickel hydrogen window was applied in a sodium heat pipe. With this measure the inactive length could be limited to 25-31% of the heat pipe length in hydrogen atmosphere. (C) 2015 Elsevier Ltd. All rights reserved.