Purpose To investigate and provide objective documentation of the possible differences in the axonal reinnervation process of facial muscles after hypoglossal-facial nerve anastomosis. Then, to search for the presence of the trigemino-hypoglossal reflex and determine whether it indicates better peripheral recovery. Methods Electrophysiological examination performed on 20 patients who had undergone VII-XII anastomosis, with follow-up periods of more than 2 years. Results The mean follow-up time after surgery was 4.1 +/- 1.3 years (range 2-8 years). The degrees of axonal reinnervation for the orbicularis oculi (OOc) and orbicularis oris (OOr) were 46.91 +/- 19.77 and 32.65 +/- 14.85, respectively. And the difference between these muscles was statistically significant (p = 0.018) in favor of the OOc. In addition, R1 blink reflexes that were not followed by R2 components were observed in 30% of the patients. However, these 6 patients with short-latency potential did not differ from the others in terms of latency, the amplitude of compound muscle action potential (CMAP), and degree of axonal reinnervation (p > 0.05) at both muscles (OOc and OOr). Conclusion The recoveries of the lower face and upper face are different after VII-XII anastomosis, and in our patients the OOc healed better. In addition, R1 blink reflexes that were not followed by R2 components were observed in 30% of the patients. However, the patients with these blink reflexes did not have better peripheral healing in their neuromuscular units, which suggests that the blink reflex is not an indicator for peripheral recovery.