Cyclooxygenase-2 (COX-2) may increase prostaglandin E(2) (PGE(2)) production in central nervous system (CNS) and contribute to the severity of pain responses in inflammatory pain. In this chapter, we sought to evaluate the possible role of COX-2 induction and prostaglandins (PGs) synthesis within neuronal areas proposed to be involved in migraine genesis in the animal model of migraine based on the administration of systemic nitroglycerin (NTG). Male Sprague-Dawley rats were injected with NTG (10mg/kg, i.p.) or vehicle and sacrificed 2 and 4h later. The hypothalamus and the lower brain stem were dissected out and utilized for the evaluation of COX-2 expression by means of Western blotting and for the determination of PGE(2) levels by means of ELISA immunoassay. COX-2 expression increased in the hypothalamus at 2h and in the lower brain stem at 4h. PGE(2) levels showed an opposite pattern of change with a decrease in PGE(2) levels at 2h in the hypothalamus and an increase at 4h in the lower brain stem. These data support the hypothesis that NTG administration is capable of activating the COX-2 pathway within cerebral areas. This activity may explain the pronociceptive effect of NTG described in animal and human models of pain. Most importantly, these findings point to mediators and areas that may be relevant for migraine pathogenesis and treatment.