The aim of this study is to estimate the unexplained gender pay gap in individual departments of a Czech hospital, to find out whether this gap varies between departments and, if so, to identify the possible causes of these differences. To estimate the unexplained part of the gender pay gap, we use the average treatment effect on the treated (ATT), and to identify the causes behind differences in the unexplained gender pay gap we use a linear regression model. We find that the ATT varies significantly between departments. To explain these differences, we use selected characteristics of the departments: the department’s size, the proportion of women in the department, and the gender of the departmental head. We come to the conclusion that women’s wages increase relative to male wages as the proportion of female employees grows. On the other hand, the unexplained gender wage gap is not proven to be lower in smaller or female-led departments.