We investigated whether functional brain networks are different in coloured-hearing synaesthetes compared with non-synaesthetes. Based on resting state electroencephalographic (EEG) activity, graph-theoretical analysis was applied to functional connectivity data obtained from different frequency bands (theta, alpha1, alpha2, and beta) of 12 coloured-hearing synaesthetes and 13 non-synaesthetes. The analysis of functional connectivity was based on estimated intra-cerebral sources of brain activation using standardized low-resolution electrical tomography. These intra-cerebral sources of brain activity were subjected to graph-theoretical analysis yielding measures representing small-world network characteristics (cluster coefficients and path length). In addition, brain regions with strong interconnections were identified (so-called hubs), and the interconnectedness of these hubs were quantified using degree as a measure of connectedness. Our analysis was guided by the two-stage model proposed by Hubbard and Ramachandran (2005). In this model, the parietal lobe is thought to play a pivotal role in binding together the synaesthetic perceptions (hyperbinding). In addition, we hypothesized that the auditory cortex and the fusiform gyrus would qualify as strong hubs in synaesthetes. Although synaesthetes and non-synaesthetes demonstrated a similar small-world network topology, the parietal lobe turned out to be a stronger hub in synaesthetes than in non-synaesthetes supporting the two-stage model. The auditory cortex was also identified as a strong hub in these coloured-hearing synaesthetes (for the alpha2 band). Thus, our a priori hypotheses receive strong support. Several additional hubs (for which no a priori hypothesis has been formulated) were found to be different in terms of the degree measure in synaesthetes, with synaesthetes demonstrating stronger degree measures indicating stronger interconnectedness. These hubs were found in brain areas known to be involved in controlling memory processes (alpha1: hippocampus and retrosplenial area), executive functions (alpha1 and alpha2: ventrolateral prefrontal cortex; theta: inferior frontal cortex), and the generation of perceptions (theta: extrastriate cortex; beta: subcentral area). Taken together this graph-theoretical analysis of the resting state EEG supports the two-stage model in demonstrating that the left-sided parietal lobe is a strong hub region, which is stronger functionally interconnected in synaesthetes than in non-synaesthetes. The right-sided auditory cortex is also a strong hub supporting the idea that coloured-hearing synaesthetes demonstrate a specific auditory cortex. A further important point is that these hub regions are even differently operating at rest supporting the idea that these hub characteristics are predetermining factors of coloured-hearing synaesthesia.