This paper discuss some concern and challenges regards with the U.S-Mexico transborder cooperation, especially with the role of Mexican local governments to manage the transnational border issues, such as drug trafficking, public security and terrorism. The paper examines two main concerns: first, an overview on transborder cooperation along the U.S. Mexican border, focusing in the Tijuana San Diego region on matters relating to narcotrafficking, public security and terrorism and second, some border impacts on the Mexican local governments under the U.S. border security policy.