In September 2006 his daughter was sponsored by Felipe Calderon and Margarita Zavala in Torreon, at that time Guillermo Anaya's sister was the wife of Sergio Villareal el Grande's brother, who attended the meeting and recommended Calderon to appoint Genaro Garcia Luna as head of security.

On October 15, 2007, the then governor of Coahuila, Humberto Moreira, who is currently facing harsh criticism for the illicit debt of the state of Coahuila, accused him, together with Senator Ernesto Saro Boardman and the national president of PAN, Manuel Espino, of having links with drug trafficking,[3] which was denied by the senator who demanded Moreira to prove it or retract it, otherwise he would proceed to sue him criminally.

[4] Semanario Proceso published a column allegedly confirming Senator Anaya's family ties with one of the main lieutenants of the Gulf Cartel.

However, a defamation lawsuit was filed against the author of said article, which resulted in a ruling in favor of Guillermo Anaya in which the accusations were proven to be false.

[6] In 2011 he was candidate for governor for the parties Acción Nacional and Unidad Democrática de Coahuila, in the electoral process to renew the governorship of Coahuila in the elections of that year being defeated by Rubén Moreira Valdez, brother of the then governor on leave of absence Humberto Moreira.