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Motifs are patterns of inter-connections between nodes of a network, and have been investigated as building blocks of directed networks. This study explored the re-organization of 3-node motifs during loss and recovery of consciousness. Nine healthy subjects underwent a 3-h anesthetic protocol while 128-channel electroencephalography (EEG) was recorded. In the alpha (8–13 Hz) band, 5-min epochs of EEG were extracted for: Baseline; Induction; Unconscious; 30-, 10- and 5-min pre-recovery of responsiveness; 30- and 180-min post-recovery of responsiveness. We constructed a functional brain network using the weighted and directed phase lag index, on which we calculated the frequency and topology of 3-node motifs. Three motifs (motifs 1, 2 and 5) were significantly present across participants and epochs, when compared to random networks (p < 0.05). The topology of motifs 1 and 5 changed significantly between responsive and unresponsive epochs (p-values < 0.01; Kendall’s W = 0.664 (motif 1) and 0.529 (motif 5)). Motif 1 was constituted of long-range chain-like connections, while motif 5 was constituted of short-range, loop-like connections. Our results suggest that anesthetic-induced unconsciousness is associated with a topological re-organization of network motifs. As motif topological re-organization may precede (motif 5) or accompany (motif 1) the return of responsiveness, motifs could contribute to the understanding of the neural correlates of consciousness.