One of the issues encountered in Reconfigurable Manufacturing Systems (RMS) is related to the evaluation and selection of a new configuration among a set of available alternatives to meet unexpected and unpredictable changes/disturbances. Configurations are often evaluated using indicators that are mainly related to performances of technical components of a manufacturing system, assuming that the working environment is safe and healthy. Unfortunately, this assumption is often unrealistic, since it does not take into account some arduous working conditions (such as sustained physical or mental efforts, heavy noise, etc.), which may lead to high instances of sickness leave, inability to operate some equipment, damage to equipment or products, etc. Thus, the best configuration, selected based on product or equipment performance only, can turn out to perform poorly if, for example, required operators are absent or less productive than expected. In this paper, we suggest some human factors and ergonomics related indicators that allow taking into account arduousness of working conditions when reconfiguring a manufacturing system. An Analytic Hierarchy Process (AHP) is developed to assist decision makers in selecting configurations based on both technical and human performance. The results of our experiments show the importance of considering such human factors and ergonomics issues in reconfiguring manufacturing systems.