Migraine is a very common and incapacitating condition. We chose to assess the therapeutic effect of Botulinum toxin injection on migraine and tension-type headache patients in an effort to measure salivary alpha amylase for these groups before and after treatment with Botulinum toxin injection because stress appears to be a significant provoking factor of this disorder. There were twenty patients with chronic tension-type headaches and twenty-five patients with chronic migraines among the forty-five individuals. Enzyme-linked immunosorbent assay (ELISA) kits were used to test the salivary biomarker (salivary cortisol and salivary alpha amylase). The PREEMPT (Onabotulinum toxinS AntIpOde for chronic migraiNe) treatment protocol, a systematic procedure for treating chronic migraines, was administered to the patients. Biomarkers measured during the study were analyzed as surrogate measures of stress to shed light on potential physiological action of the intervention. Context In patients with chronic migraine and tension-type headaches, the effect of Nabota (Botulinum toxin type A) on specific stress-related indicators was evaluated. The results demonstrated a statistically significant (p<0.05) rise in salivary cortisol and a statistically significant (p<0.05) decrease in salivary alpha amylase following Botulinum toxin intervention for both research groups (chronic migraine, chronic tension headaches).