They were arguably two of the best pitchers of their generation, but the perception that Martinez was the more dominant pitcher persists despite Clemens having better statistics and seven Cy Young Awards, because Martinez's name was never associated with performance-enhancing drugs.
In fact, Martinez has always been outspoken about players accused of using PEDs, but his stance has softened a bit, especially when it comes to Clemens.
Their relationship changed during a dinner conversation in 2012.
That season marked the 100th anniversary of Fenway Park. The Boston Red Sox held a season-long celebration honoring the ballpark's storied history. On one particular night, the Red Sox honored the 2004 World Series team and other Red Sox greats.
Afterward, the former players held a private dinner. Martinez, Clemens, Tim Wakefield and Jason Varitek sat alone, and their conversation became "intense," as one former player who witnessed the sit-down described it.
Martinez and Clemens not only broke bread that night, they set their egos aside and mended their relationship.
"It was the first time we kind of went back and forth as people, as pitchers and as men and how we approached the game," Martinez said Thursday night. "He told me how he would train, how dedicated he is to mastering his craft. That's when I really got to feel pretty much how Roger was away from the game and why he competed the way he competed. That gave me total satisfaction to get to know him. We are very, very similar as far as approaching the game and taking responsibility for the game."
Earlier in the day, Clemens admitted he and Martinez talked about the difference between being a power pitcher and a power thrower. Some in attendance that night in 2012, however, believe it was a new beginning for Clemens and Martinez.
Now they have a totally different relationship.
"Yeah, it is [different]," Martinez said. "I'm supportive, and I've always said, honestly, I believe Roger Clemens was a Hall of Famer way before all of these things were said. I was a big fan of Roger's in the '80s, the era when I was really falling in love with baseball. That was the time I got to see the best out of Roger and I was a huge fan."
On Thursday, Martinez and Clemens, along with Nomar Garciaparra and broadcaster Joe Castiglione, were inducted into the Red Sox Hall of Fame.
Martinez went out of his way to goof around with Clemens, pretending to interview him while a horde of media surrounded them. It seems Martinez wants everyone to know he no longer has any issues and he's trying to help clear Clemens' name and help him reach the Hall of Fame.
"With all due respect to everybody that votes, I'll have to say Roger and Barry Bonds are two guys that I think had enough numbers before anything came out to actually earn a spot in the Hall of Fame," Martinez said. "I'm not quite sure 100 percent how close they will be before all the things came out, but in my heart, if you asked me before any of that, I would've said, 'Yes, 100 percent,' without looking back.
"It wasn't just the individual performances. [It was] how they dominated the time that they came up and stayed in the big leagues until those things happened. I believe they have a legit chance, and I think, with time, the voters will take into consideration what they did previously."
Martinez is a smart man. His comments about Clemens were subtle but to the point. The two had some intense battles on the mound during their respective careers, but now there seems to finally be a mutual respect, especially from Martinez.
So, is the National Baseball Hall of Fame a possibility for Clemens?
"I have zero control over that, so if that happens it would be great," Clemens said.
He has been on the Hall of Fame ballot, which is voted on by the Baseball Writers' Association of America, in each of the past two years, but Clemens has received well below the required 75 percent needed for induction. Last year, he earned only 35.4 percent of the vote.
His career has been tainted by the fact his name has been associated with the use of performance-enhancing drugs. On paper, he's no doubt one of the best pitchers of all time, winning seven Cy Young Awards, posting 354 wins and striking out 4,672 during a 24-year career.
When asked whether or not it's a disappointment he's not in the Hall of Fame, Clemens said it wasn't.
"I don't know if it's that important," he said. "It's not going to change me as a person. I tell people I've got bits and pieces of us there now. We go visit those people and they're great to us, but it's not something I sit up and worry about every day.
"I'm far too busy to worry about something like that. I know what I did in my career and how I did it, and I did it right. I can't control what people think or people that don't look at facts."
Either way, Clemens said the Red Sox franchise would always have a piece of his heart.
For Clemens, Thursday's induction into the Red Sox Hall of Fame was a high point since his final retirement after the 2007 season. Clemens has returned to Fenway numerous times since he retired. Each time, the ovation becomes louder and louder. It was no different Thursday night.
"This is my home. This is where I got started," he said.
After Thursday's Red Sox Hall of Fame induction ceremonies, Clemens spent the afternoon throwing batting practice to two of his four sons -- Koby and Kody -- on the field at Fenway. Even at age 52, Clemens looks like he could still pitch in the big leagues.
Clemens spent 13 seasons with the Red Sox after the team selected him in the first round (19th overall) in the 1983 MLB draft. After he left Boston, he played for the Toronto Blue Jays, New York Yankees and Houston Astros.
In retirement, his reputation took a hit due to allegations of steroid use. Even though the Red Sox finally honored him for his on-field accomplishments, Clemens believes the fans have always paid him tribute.
"Well, I've been honored for it for a long time," he said of his career accomplishments. "I hear it from fans every day, even in retirement."
The Red Sox have retired seven numbers, including Joe Cronin (No. 4), Bobby Doerr (1), Carlton Fisk (27), Johnny Pesky (6), Jim Rice (14), Ted Williams (9) and Carl Yastrzemski (8). Also, Jackie Robinson's No. 42 is officially retired by Major League Baseball.
Since Clemens left the Red Sox, no other player has worn No. 21, but the Red Sox have not officially retired the number.
"It would be great," Clemens said. "If it happens, it happens. It's not going to change me as a person. It's not why I played the game. When I was out there and doing it, I did it to the best of my ability and I worked my tail off. If it happens, it happens. It's totally up to these guys."
Clemens said being inducted into the Red Sox Hall of Fame is an honor. He might have dismissed his absence from Cooperstown, but when Martinez vouches for him, it's an indication that their relationship has changed.
"It's not a subject that people bring up, people that I'm around the most," Clemens said of Cooperstown. "It's something you have no control over. I did it. I did it to the best of my ability and I did it the right way. If other people want to, again, I can't control what other people think. Regardless, today's not going to change me as a person, [Cooperstown] wouldn't change me as a person or how I live my life. I'm going to enjoy today and give thanks to the people I know helped my path come through Boston."
Martinez is now on that list.