Atilano spent the beginning of the 2006 season pitching for the Myrtle Beach Pelicans of the high A-levelCarolina League, where he accrued a win-loss record of 6–7 and an ERA of 4.50 in 18 starts and 1 relief appearance. After struggling at the beginning of the season, he went 3–0 with a 2.89 ERA in July. He pitched two complete games for Myrtle Beach during 2006, but an elbow injury suffered in early August ended his season.
Atilano was recalled from Triple-A Syracuse, by the Nationals, to replace injured Jason Marquis on April 22, 2010. He allowed one run on five hits in a 5–1 Nationals victory against the Los Angeles Dodgers on April 23, 2010, his first major league start and first major league win. He started off the season well, going 5–1 in his first six decisions—which included consecutive victories over Tim Lincecum and Roy Oswalt. But then he fell to 6–7 with a 5.15 ERA, and underwent surgery in July to remove bone chips in his elbow. At the start of Spring Training in February 2011, he was designated for assignment and removed from the 40-man roster.
On December 9, 2011, he signed a minor league contract with the Cincinnati Reds, and he played for their organization through the 2012 season. Atilano lives in San Juan, Puerto Rico.