We comment on a recent article published in Brain Connectivity (Hatz et al., ) that combined electroencephalography (EEG) microstate analysis with the phase-locking index (PLI) and found that the test–retest reliability of connectivity patterns as obtained by the PLI increased when the data had been previously parcellated into microstates. Although we acknowledge the need to parcellate the continuous data into periods that supposedly correspond to transiently stable patterns of connectivity, we believe that the approach chosen by the authors is seriously mistaken. In particular, their approach disregards the particular a priori assumptions contained in each of the two methods that define connectivity in specific terms. Unfortunately, for microstate analyses and the PLI, these definitions are mutually exclusive, which makes attempts to draw any coherent conclusion in terms of comprehensibly interlinked biological processes meaningless. The occurrence of this type of problems should draw the attention to the importance of the particular methodological and conceptual features and limitations that come with the specific a priori assumptions contained in any quantifier of brain functional connectivity.