Pirates righthander Brad Lincoln was lost for the season after having Tommy John surgery on Tuesday. Lincoln, the fourth overall pick in 2006, pitched just 24 innings between the Rookie-level Gulf Coast League and low Class A Hickory before being shut down with a strained oblique that hampered him through instructional league last fall.

Dr. James Andrews performed the ligament replacement surgery, which was deemed a success, in Birmingham, Ala.

“Obviously this is an inherent risk with pitchers,” Pirates general manager Dave Littlefield said. “First, I feel badly for Brad, who I’m sure is going to have a long career in the major leagues. This should be a short setback for him in the long run.

“He had some discomfort at the end of last season, and then this spring he was throwing fine off flat ground. When he moved to the mound, he had discomfort again. We shut him down and did some testing–he’d essentially failed two throwing programs, so Dr. (James) Andrews went in and discovered the ligament was insufficient and recommended surgery.”

Lincoln, who signed for $2.75 million out of Houston, took a month off before reporting to Bradenton, Fla., to begin his pro career in early July. He’d thrown 128 innings at Houston last spring before the Pirates took him fourth overall.

But the scouting and player-development departments aren’t necessarily to blame for Lincoln’s injury. All medical reports were clear on Lincoln when the Pirates drafted him, and the player-development staff limited his pitch count within those 24 innings and wound up shutting him down after the oblique strain. And when they fired him up again during instructs, Lincoln’s elbow came up tender–though he didn’t say anything to the Pirates’ brass at the time.

The problem, however, is the history.

Lincoln is the latest in a litany of Pirates first-rounders to go through major arm surgeries as they moved through the system. Lefthander Sean Burnett (19th overall, 2000), and righthanders John Van Benschoten (eighth overall, 2001) and Bryan Bullington (first overall, 2002) all lost significant time to arm injuries–though Lincoln is the first pitching prospect to need surgery before reaching the big leagues. Between the four pitchers, the combined signing bonus investment is over $10 million.

Burnett, Van Benschoten and Bullington currently make up the bulk of the Triple-A Indianapolis rotation, and as Littlefield was quick to point out, the Pirates have also four young starters in the big leagues that came through the system doing well. One of them was also a first-rounder, lefthander Paul Maholm.

“As the Pittsburgh Pirates organization, we have to be accountable,” Littlefield said. “It’s our responsibility to eliminate injuries as much as we can–one (pitcher getting hurt) is too many, and it’s the high profile ones that get a lot of attention.

“By no means do I deem this acceptable whatsoever. We’re certainly not happy about it, and as I oversee baseball operations, I take full responsibility. We need to do anything and everything we can to help us avoid these types of things in the future.”

As for Lincoln, it will be at least 16 weeks before he can begin a throwing program barring any setbacks. If he recovers according to schedule, he could be ready for instructional league.