Objective: Management control systems (such as budgets or balanced scorecards) are formal procedures used by managers to promote employee behavior aligned with organisational objectives. Employees may react to these control systems by either becoming more motivated or perceiving them as a threat. The aim of this paper is to determine the extent to which hospital ownership (public or private), professional group (physician, nurse, pharmacist or administrative employee), type of contract (fixed or temporary), gender and tenure can condition employee reaction to management control systems. Methods: We conducted the study in the three largest hospitals in the State of Santa Catarina (Brazil), two public (federal and state-owned) and one private (non-profit organisation). Physicians, nurses, pharmacists and administrative employees received a questionnaire between October 2013 and January 2014 concerning their current perceptions. We obtained 100 valid responses and conducted an ANOVA variance analysis. Results: Our results show that the effect of management control systems on employees differs according to hospital ownership, professional group and type of contract. However, no significant evidence was found concerning gender or tenure. Conclusions: The results obtained contribute to creating specific knowledge on the reactions of employees to the use of management control systems in hospitals. This information may be important in adapting management control systems to the characteristics of the hospital and its employees, which may in turn contribute to reducing dysfunctional worker behavior.