The actor took to Twitter claiming Clooney, 56, was to blame for her being "blacklisted" from the popular drama series in 1995, after she complained about sexual harassment on the sets.
Marquez, 48, retweeted an article in which Clooney spoke out against Harvey Weinstein and the many sexual misconduct allegations that have come out about him this week.
Clooney, who played Douglas Ross on the show, has now responded to her claims saying he did not even know Marquez was blacklisted in the first place.
He continued, "If she was told I was involved in any decision about her career then she was lied to. The fact that I couldn't affect her career is only surpassed by the fact that I wouldn't."
Marquez played nurse Wendy Goldman on the first three seasons of the NBC show.