Lyophilisation is a well-established method for drying of various substances with a wide range of applications in the pharmaceutical area. During the last decade its relevance increases with a number of therapeutically used proteins. A sensitive protein drug may undergo several changes, like unfolding and loss of activity due to various stresses during the lyophilisation process. Understanding of these processes (freezing, primary drying, secondary drying) is fundamental for manufacturing of a drug product with desired properties, namely its safety and efficacy. In order to reduce costs and increase the quality, new technologies are being rapidly developed and established in industrial lyophilisation (e.g. process analytical technologies, control nucleation techniques).