Electroencephalography (EEG) coherence analysis, based on measurement of synchronous oscillations of neuronal clusters, has been used extensively to evaluate functional connectivity in brain networks. EEG coherence studies have used a variety of analysis variables (e.g., time and frequency resolutions corresponding to the analysis time period and frequency bandwidth), regions of the brain (e.g., connectivity within and between various cortical lobes and hemispheres) and experimental paradigms (e.g., resting state with eyes open or closed; performance of cognitive tasks). This variability in study designs has resulted in difficulties in comparing the findings from different studies and assimilating a comprehensive understanding of the underlying brain activity and regions with abnormal functional connectivity in a particular disorder. In order to address the variability in methods across studies and to facilitate the comparison of research findings between studies, this paper presents the structure and utilization of a comprehensive hierarchical electroencephalography (EEG) coherence analysis that allows for formal inclusion of analysis duration, EEG frequency band, cortical region, and experimental test condition in the computation of the EEG coherences. It further describes the method by which this EEG coherence analysis can be utilized to derive biomarkers related to brain (dys)function and abnormalities. In order to document the utility of this approach, the paper describes the results of the application of this method to EEG and behavioral data from a social synchrony paradigm in a small cohort of adolescents with and without Autism Spectral Disorder.