We aim to demonstrate possible autonomic dysfunction based on salivary α-amylase measurements during and after the vertigo attacks associated with Ménière disease (MD) and benign paroxysmal positional vertigo (BPPV). Patients admitted to the emergency room with a diagnosis of vertigo attacks caused by either MD (n = 15) or BPPV (n = 9) constituted the study groups. The control group (n = 10) consisted of volunteer patients admitted to the emergency department with minor soft-tissue trauma. The first saliva samples were obtained immediately during the attacks and the second and third samples were obtained on the third and fifteenth days of the attack, respectively. In the controls, the first sample was obtained after admission to the hospital and the second sample was obtained on the third day. Salivary α-amylase levels were evaluated. The difference between salivary α-amylase levels in patients with MD and BPPV was not significant. The amylase value measured early after the BPPV attack was significantly lower than that of the controls (p = 0.008). Although not significant, an undulating pattern of salivary α-amylase levels was observed with both diseases. An autonomic imbalance could be partly demonstrated by salivary α-amylase measurement early after the attack in patients with BPPV. Therefore, amylase may be a promising marker that is worth further investigation.