Introduction: In this study we explored brainstem reflex excitability changes, blink reflex recovery cycles (BRRCs), and masseter inhibitory reflexes (MIRs) in patients with amyotrophic lateral sclerosis (ALS). Methods: Fourteen ALS patients and 14 healthy control subjects were recruited. The BRRC was examined at interstimulus intervals (ISIs) of 100, 200, 300, 400, 500, and 600 ms. The latencies and durations of silent period 1 (SP1) and silent period 2 (SP2) of the MIR were measured. Results: Decreased R2 area suppression was prominent in the ALS group at ISIs of 200, 300, and 400 ms (P < 0.02), whereas no significant differences between groups at 100, 500, and 600 ms ISIs (P > 0.05) were observed. SP2 duration was significantly prolonged in the ALS group compared with controls (P = 0.01). Conclusions: Brainstem inhibitory and excitatory interneuronal activity is altered in ALS, possibly brought about by physiological and morphological changes at the cortical or bulbar levels.