Mark Berry, Lookouts manager, praised Williamson's performance: "I was highly impressed...I expected him to be more erratic because of Smoltz, the big crowd and the whole situation.

"[4] Williamson would start just eighteen games for the Lookouts that year after battling injuries, but at the end of the season Cincinnati promoted him to the Triple-A Indianapolis Indians.

Cincinnati planned to call Williamson up in September, but he "stretched a tendon in the middle finger of his pitching hand" during a game for Indianapolis that ended his season.

[5] Cincinnati invited Williamson to spring training in 1999, where the combination of an impressive performance and injuries to key members of the pitching staff, including Denny Neagle and Stan Belinda, led to Williamson making the major league club despite having made just five appearances at the Triple-A level and never being on the 40-man roster.

He made fewer appearances than in 1999 but pitched more innings, due in part to joining the starting rotation after the All-Star break.

[10] After a lackluster spring training, Cincinnati returned Williamson to the bullpen, who would make just two appearances before going on the disabled list with a torn ligament in his shoulder.

After consultation with orthopedic surgeon James Andrews, Williamson underwent Tommy John surgery, ending his season.

[12] On July 31, 2003, Cincinnati traded Williamson to the Boston Red Sox for Phil Dumatrait, Tyler Pelland and cash.

[17]The mid-season arrival of Williamson, along with Scott Sauerbeck, Jeff Suppan and Byung Hyun Kim was expected to boost an already strong Boston team to the 2003 World Series.

[19][20][21] Williamson returned to Boston in 2004 as a middle reliever and got off to a strong start (1.69 ERA in 14 appearances) before elbow tendinitis placed him on the disabled list again in late May.

[22] Williamson returned in mid-June, but never felt completely healthy and went back on the DL at the beginning of July with a nerve impingement in his right forearm.

"[24][25][26] In August Boston placed Williamson on the 60-day disabled list as word spread that he might undergo a second Tommy John surgery, which would end the 2004 season and likely preclude any activity in 2005 as well.

[28] Williamson filed for free agency at the end of the season, and departed the organization after Boston declined to offer arbitration.

[36] Williamson returned at the end of June and pitched in eight more games, but on July 22 Chicago traded him to the San Diego Padres for minor League pitchers Fabian Angulo and Joel Santo.

"[38] In an interview with the Galveston County Daily News, Williamson also expressed disappointment at the way Chicago manager Dusty Baker had used him and revealed that he had considered retiring altogether.

"[39] Just days after that interview was published, Williamson made his last appearance for San Diego: an MRI revealed a bone chip in his elbow.

[43] Williamson returned in June and appeared in ten more games, but lingering questions about his health and a desire on the part of Baltimore's management to promote younger players led to him being designated for assignment on July 4.

On January 24, 2009, Williamson signed a minor league deal with the Detroit Tigers, who were looking for middle relievers after a disappointing 2008 season.