This chapter discusses the origin of Colombia’s military criminal code in emergency decrees and the decades-long military jurisdiction over human rights cases that followed. This chapter traces a shift from prior years of government impunity to a period in the mid-late 1990s when human rights prosecutions emerged and steadily increased over time. As a result of two key factors, judicial review of emergency legislation and judicial independence among judges on the Constitutional Court, the military criminal code was altered, prosecutions were steadily transferred from military courts to ordinary courts, and the number of prosecutions increased.