Among musicians, Morgenstein is widely known for his work with the Dixie Dregs. The band, led by guitarist Steve Morse, formed in the middle 1970s while Morgenstein and the rest of the band were students at the University of Miami. With virtually no radio support, but a great word-of-mouth reputation, the band became a force to be reckoned with. The Dregs received Grammy nominations for each of their last six recordings and much coverage in music trade magazines throughout the 1980s. Modern Drummer magazine named Morgenstein Best Progressive Rock Drummer for five consecutive years. Rod was also voted Best All-Around Drummer in their 1999 reader's poll.

After the Dregs disbanded, Morgenstein continued touring and recording with the three-piece Steve Morse Band until 1986, when Morse took a gig with the group Kansas. Out of work for the first time since college, Morgenstein struggled a bit before surfacing as a member of the soon-to-be platinum-selling pop metal band Winger.

Since Winger, Morgenstein has worked with progressive rock groups like Platypus, Jazz Is Dead and the Rudess Morgenstein Project. As a teacher at Berklee, Morgenstein's reputation precedes him. "A lot of the students who come to me are fans of the groups I've been in," he said. "Some want to study the heavy metal style I played with Winger and others are interested in the fusion style that I played with the Dregs. I have written over 200 columns for drum magazines, and will soon have a book of drum set warm-ups published by Berklee Press, so there is always plenty to work on.

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