The evaluation of the level of spatial uncertainty builds theoretically on fuzzy set theory and the premise that the affinity of a basic spatial unit may assume values along a continuum between zero and full affinity. The paper briefly presents the motivation for the evaluation of fuzziness in functional regions based on daily travel-to-work flows. It discusses the existing measures of affinity and proposes a new approach to evaluate the fuzzy nature of functional regions. The proposed methodological innovations are tested using the example of the two-tier hierarchical system of functional regions in the Czech Republic.