Following the disappointing 2005 season, it was clear major changes needed to be made within the Orioles. In the front office, Executive VP Jim Beattie was not re-signed, allowing Mike Flanagan to become the sole GM of the Orioles. Shortly after, Jim Duquette was hired as Vice President of Baseball Operations, which was Flanagan's previous position. Duquette made it clear at his signing that he reported to Flanagan, so the "two-headed GM" did not exist anymore. The Orioles also fired Assistant General Manager Ed Kenney and asked for the resignation of Dave Ritterpusch, Director of Baseball Information Systems.
The roster changes of 2005 were prefaced with Peter Angelos' comments: "We are coming back strong next year. I know you have heard that tune before, but this time it will literally come true." The Orioles allowed Rafael Palmeiro, Sammy Sosa, and B.J. Surhoff to become free agents. They also set their wishlist: An everyday first baseman, an experienced starter, a closer, a defensive catcher, outfield help, more defense, and more speed. However, their offseason moves showed no differences from past years. The Orioles were not able to re-sign closer B. J. Ryan, who signed a landmark deal with the Toronto Blue Jays. They were also locked out in bids to sign first baseman Paul Konerko, outfielder Johnny Damon, and starter Paul Byrd. The Orioles chose not to enter the bidding for players like A. J. Burnett and Kevin Millwood, whose asking prices were far beyond what the Orioles were willing to pay, but they did sign catcher Ramón Hernández. Locked out of pursuits to sign top-tier players, the Orioles decided to make several moves to allow minor league prospects more time to develop. This led to bringing in players like Jeff Conine and Kevin Millar, both of whom are known for their positive presence in the clubhouse. On February 4, 2006, Ricky Bottalico was signed as a Free Agent with the Baltimore Orioles. The Orioles also made several trades to bring in needed players. They first traded disgruntled reliever Steve Kline for LaTroy Hawkins, then traded for outfielder Corey Patterson, who brought speed and defense to the outfield, and traded former closer Jorge Julio and John Maine for experienced starter Kris Benson. The Orioles also addressed future free agents by extending the contract of outfielder Jay Gibbons and third basemanMelvin Mora, and recently signed a contract extension with second baseman Brian Roberts. The team's Opening Day roster featured top prospect Nick Markakis, a potential A.L. "Rookie of the Year", the best young position player the Orioles' farm system has produced since Brian Roberts. Markakis represents the revival of the Orioles' farm system, which features four players listed in Baseball America's 2006 list of the top 100 prospects in minor league baseball.
During spring training in 2006, the Nationals and Orioles played each other in Washington on March 31 and in Baltimore on April 1. The first match up of the Beltway Series rivalry took place on May 19, 2006 during the 2006 regular season, the Orioles won at RFK Stadium. This marked first time in 35 years that the Orioles played a regular-season game in Washington, as they played the Washington Senators, another team in the American League annually from 1954 to 1960. The Orioles continued that rivalry with the new Washington Senators from 1961 to 1971. The two teams split the season series 3-3 with each time winning two games at home and one on the road.
