Friday was the deadline to set 40-man rosters prior to the Rule 5 Draft, which will be held Dec. 8 at the Winter Meetings in Dallas. The Astros also re-signed right-hander Lance Pendleton to a Minor League contract with an invitation to Spring Training.
By purchasing the contract of Clemens, the Astros' 40-man roster stands at 38.
"At this stage, we want to have some flexibility to add a free agent or take a swipe at somebody in the Rule 5 Draft," Astros general manager Ed Wade said.
The Rule 5 Draft was implemented to prevent teams from stockpiling too much young talent in their Minor League systems. Players who are eligible to be taken are those who aren't on the 40-man roster and were signed at age 19 or older and have been in the organization for four years, or were signed at 18 or younger and have been in the organization for five years.
The players selected by another club must remain on that team's active roster for the entire following season or be offered back to their original club for $25,000.
Among the players in Houston's organization not on the 40-man roster who will be eligible to be selected in the Rule 5 Draft are pitchers Danny Meszaros, Xavier Cedeno, Sergio Perez and Kyle Greenwalt, outfielders Brandon Barnes, Jon Gaston, Collin DeLome and T.J. Steele and infielder Kody Hinze.
"We talked to a lot of our people here about their feelings about candidates for protection, and I always try to hold it to the premise that any player taken in the Rule 5 Draft has to stay with the club for an entire season," Wade said. "When you do that, it lends some clarity to your decision making. It's tough to carry a guy."
The Astros did just that last year, selecting right-hander Aneury Rodriguez in the Rule 5 Draft from Tampa Bay and keeping him on the active roster for the entire season. They also took Pendleton from the Yankees in that same Rule 5 Draft, but sent him back to New York at the end of Spring Training.
Pendleton wound up being claimed off waivers by the Astros late in the season and has chosen to re-sign to a Minor League deal with his hometown club.
Adding a player to the 40-man roster means his waiver clock begins to tick, and if you protect a player in Class A ball, by the time he gets to Triple-A there's a good chance he'll be out of options and you could lose him on a $20,000 waiver claim.
"It's not an easy exercise to go through, but as we continue to build depth in the farm system and we start losing players in the Rule 5 Draft, at that point that's an indication we're where we need to be," Wade said.
Clemens, 23, posted an 8-7 record and a 3.81 ERA in 26 starts between Double-A Mississippi (20 games), Double-A Corpus Christi (five games) and Triple-A Oklahoma City (one game) last season. There are those in the organization who believe he will pitch in the big leagues next year.
Pendleton, 28, compiled a 6.75 ERA in 15 relief appearances for the Astros and Yankees last season. He spent most of his season with Triple-A Scranton/Wilkes-Barre, going 3-4 with a 3.11 ERA in 18 games, including 10 starts.
Pendleton is the ninth non-roster player, and third pitcher, to receive an invite to the Astros' Major League Spring Training camp.