Background Coherence analysis examines the functional connectivity of cortical regions, which are important for cognitive functioning and may be related to the benefits of meditation. Meditation analysis to date has analyzed coherence by comparing EEG wave power using Fast Fourier Transform (FFT), and then calculating the coherence spectra with disregard to wave phase. This method can show spurious coherence between regions that are unlikely to be synchronized. Our methods used a phase synchronization measure of coherence, mean phase coherence (MPC) - novel to meditation. Methods Attentional performance before and after 20-minute eye-closed focused attention meditation was measured in 25 healthy, meditation naïve subjects. MPC was calculated in wave specific bins and for every 30 seconds during meditation. To determine if these EEG hallmarks showed relation with performance changes, MPC and power was then correlated to PVT results. Results MPC showed high alpha coherence between front-temporal and frontal-occipital electrodes. Meditation also underwent temporal changes with high prefrontal gamma coherence correlated with better performance at meditation onset, with frontal alpha and beta power later in the meditation. Alpha coherence throughout the meditation was correlated with better attentional performance changes. Conclusions Our data suggest that MPC may have identified regions of high coherence during meditation that are correlated with improved PVT performance. The results also suggest that meditation is a dynamic neural process that requires more careful analysis into temporal changes. Finally, results suggest that “control” conditions need to be more systematically studied, as many conditions may show similar neural dynamics to meditation