The use of different objective functions in hierarchical aggregation procedures is examined in this paper. Specifically, we analyse the use of the original Intramax objective function, the sum-of-flows objective function, the sum-of-proportions-to-intra-regional-flows objective function, Smart’s weighted interaction index, the first and second CURDS weighted interaction indices, and Tolbert and Killian’s interaction index. The results of the functional regionalisation have been evaluated by self-containment statistics, and they show that the use of the original Intramax procedure tends to delineate operationally the most persuasive and balanced regions that, regarding the intra-regional flows, homogeneously cover the analysed territory. The other objective functions give statistically better but operationally less suitable results. Functional regions modelled using the original Intramax procedure were compared to the regions at NUTS 2 and NUTS 3 levels, as well as to administrative units in Slovenia. We conclude that there are some promising directions for further research on functional regionalisation using hierarchical aggregation procedures.