He played in Major League Baseball (MLB) for the Colorado Rockies, Boston Red Sox, Kansas City Royals, and Toronto Blue Jays.

A power-throwing left-hander, Morales made his Major League debut on August 18, 2007, against the Los Angeles Dodgers.

He was also part of the Rockies' 25-man active roster for the postseason where the team went to the World Series for the first time ever but lost to the Red Sox in a 4-game sweep.

He began the regular season in the starting rotation, but after struggling early he was optioned to the Triple-A Colorado Springs Sky Sox.

With the Red Sox ahead 1-0 in the 6th inning and two inherited runners on base, Morales walked Prince Fielder on 4 pitches, then fell behind Victor Martinez before yielding a 2-run Wall Ball single.

On December 18, 2013, Morales was traded back to the Colorado Rockies along with minor league pitcher Chris Martin for utility man Jonathan Herrera.

[3] After being primarily a relief pitcher for the Red Sox in his previous three years, Morales found his way back into a starting role to begin the 2014 season with the Rockies; he made his season debut on April 3 as the team's fourth starter, giving up 3 earned runs and 8 hits in 5+1⁄3 innings in a no decision against the Miami Marlins.

[4][5] Morales signed a minor league deal with the Kansas City Royals on February 19, 2015 and made the team out of spring training.

With the Royals finishing the season 95-67, the team clinched the AL Central and eventually won the 2015 World Series against the New York Mets, their first championship in 30 years.

On March 4, 2016, Morales signed a minor league deal with the Milwaukee Brewers with an invitation to spring training.