Functional regions are a generalization of changeable social and economic functional interactions in a territory. These regions are increasingly used when analysing economic, social, environmental, and spatial development and when making development-related decisions. In this doctoral dissertation we propose a procedure to evaluate the areas and the number of hierarchical functional regions. The procedure is based on: (a) using Intramax, a hierarchical method to model functional region systems of labour commuting by time intervals, (b) comparison of functional region systems using the index proposed in this dissertation, (c) evaluation of functional regions using selected indicators, and (d) evaluation of the impact of selected socio-economic factors on labour commuting in, and between, functional regions in a spatial interaction model using regression analysis. The procedure of evaluating the systems of hierarchical functional regions was employed for the case study of Slovenia for the period 2000–2011. The study pointed at three characteristic and balanced systems of functional regions, whose area and efficiency, in the light of the proportion of inner flows and homogeneity of employment and housing self-containment, did not significantly change over the period analysed. These are: a system of 5 functional regions with centres in Ljubljana, Maribor, Celje, Koper, and Novo mesto, a system of 7 functional regions with centres in Ljubljana, Maribor, Celje, Koper, Novo mesto, Nova Gorica, and Slovenj Gradec, and a system of 60 functional regions. In the dissertation we tested the assumption that the number and the areas of functional regions could be evaluated according to the socio-economic factors that significantly influence labour commuting. The analysis of the impact of the various factors most often analysed in the literature on labour commuting in, and between, functional regions highlighted four factors whose impacts proved to be statistically significant over the whole period considered and at all hierarchical levels of larger (2–70) functional regions. These factors are: travel time to work, population in origin, population in destination, and the employment rate in destination. The proposed approach allows for continuous monitoring and evaluation of balanced systems of hierarchical functional regions in the territory of Slovenia. The characteristic and balanced systems of 5 and 7 functional regions, respectively, as highlighted in this dissertation, can provide a criterion for deciding about establishing provinces in Slovenia.