Subsequently, Mendez worked for the Catholic Church in Aurora, Illinois, protecting the rights of migrant workers. In 1978, he joined the Lawyers' Committee for Civil Rights under the Law in Washington, D.C., and in 1982, he launched Human Rights Watch's (HRW) Americas Program. He continued to work at Human Rights Watch for 15 years, becoming their general counsel in 1994. He is also a visiting scholar at American University Washington College of Law's Academy on Human Rights and Humanitarian Law, a Professor of Human Rights Law in Residence at the Washington College of Law, and the Faculty Director of the Anti-Torture Initiative at the law school.
