The risks identification is a key step for the safe design of a manufacturing process and, in this framework, once the threats to the process have been pointed out, it is important to evaluate their consequences, as well as their causes. In this paper, the risk assessment has been used to build the basis for the risk-based decision making in plant and process design of a pilot scale freeze-dryer, to be then exploited in the design of a full scale safer plant, taking into account also the experimental evaluation of possible human errors.