Cortes finished the 2006 season with the Class-A Burlington Bees of the Midwest League. He went 1–2 with a 6.69 ERA with 30 strikeouts in seven games, all starts.
In 2007 Cortes played for the Class-A Advanced Wilmington Blue Rocks of the Carolina League. He went 8–8 with a 3.07 ERA with 120 strikeouts in 23 games, all starts. He was named the Carolina League Pitcher of the Week for the week of August 20 to August 26.[4] Cortes was again awarded Pitcher of the Week for the week of August 27 to September 2.[5]
He played for the Double-A Northwest Arkansas Naturals of the Texas League in 2008. Cortes went 10–4 with a 3.78 ERA with 109 strikeouts in 23 games, all starts. Before the season he was ranked as the second best prospect in the Royals' organization by Baseball America.[6][7] He was also named to the Texas League All-Star team.[8] He did miss playing time while on the disabled list.[9] The Royals recognized Cortes as the top pitcher for the Double-A Naturals and he was selected to play in the Arizona Fall League at the end of the '08 season.[10][11]
In January, 2009 Cortes received the "Paul Splittorff Pitcher of the Year Award" from the Royals.[12] He attended spring training with the Royals in '09 as a non-roster invitee.[13][14] Cortes was named a "Player to Watch" by MLB.com before the season.[15] He went 6–6 with a 3.92 ERA with 57 strikeouts in 16 games, 15 starts with the Double-A Northwest Arkansas Naturals. On July 10 he was traded by the Royals with Derrick Saito to the Seattle Mariners in exchange for Yuniesky Betancourt.[16][17]
Seattle Mariners
After the trade Cortes was assigned to the Double-A West Tenn Diamond Jaxx. Cortes went 1–5 with a 4.94 ERA and 55 strikeouts in 10 games, all starts. He was added to the Mariners 40-man roster on November 20.[18]
On December 12, 2011, the Mariners announced via their Twitter feed that Cortes had been non-tendered along with catcher Chris Gimenez.[19][20]
Washington Nationals
Cortes signed a minor league contract with the Washington Nationals on January 4, 2012. His contract was voided on February 29, after he failed his physical with the Nationals.
Arizona Diamondbacks
Cortes signed a minor league contract with the Arizona Diamondbacks on March 15, 2013.
Personal life
Cortes, who had taken a summer job at a sporting goods store, was taken bowling by his new co-workers and when he attempted to leave the bowling alley he was stabbed after trying to break up a confrontation between his co-worker and the stabber.[21] His co-worker died and Cortes was hospitalized.[21][22] He questioned if he would be able to pitch again since the injury was on his throwing arm.[21] He did however make a full recovery.[21]
I told the guys I was going to leave and they said OK, they'd come too and we started to walk out...There were three gangsters outside and they picked a fight with one of my co-workers. I tried to mellow everyone out, but I got caught up in it and two guys tried to fight me. I started fighting and I got stabbed eight times.
On January 1, 2009, Cortes was arrested on charges of public intoxication and disorderly conduct in Fayetteville, Arkansas.[23][24] According to police accounts, Cortes was arrested after he allegedly urinated on a fence outside Grub's Bar & Grille.[23][24] After five hours in jail, Cortes was released when he posted a $655 bond.[23][24]