Ellis posted a career .991 fielding percentage, the fifth-best all-time for a second baseman in MLB history at the time of his retirement.

Ellis is one of three players to have made it to the Major Leagues who played for the Rapid City Post 22 American Legion baseball program; the others are Kelvin Torve and Dave Collins.

As a 16-year-old, Ellis was the starting shortstop for the 1993 Rapid City Post 22 varsity "Hardhat" baseball team that touted a 70–5 record and won the national title in Roseburg, Oregon.

[3] He went on to play for the University of Florida Gators baseball program and was the MVP of the Gainesville regional at the 1998 College World Series.

[citation needed] Ellis was a ninth-round selection by the Kansas City Royals in the 1999 Major League Baseball Draft.

Ellis made his Major League debut on April 9, 2002, for the Athletics against the Texas Rangers, pinch-running in the eighth inning for Jeremy Giambi.

[5] He recorded his first base hit, in his first Major League start, on April 18 against the Anaheim Angels, a single to left field off of Ramón Ortiz.

In 2006 Ellis established what was, at the time, a single-season American League record for a second baseman with a .99685 fielding percentage,[9] beating the mark previously set by Brett Boone in 1997.

For the 2006 season the Rawlings Gold Glove Award for second basemen went to Mark Grudzielanek of the Kansas City Royals, who finished with a lower fielding percentage of .994, though won the award as a result of winning the vote of MLB managers and coaches; Ellis’ single-season record was broken the following year by Plácido Polanco of the Detroit Tigers, who made no errors during the season for a perfect fielding percentage of 1.000.

Ellis missed most of the A's 2006 post-season due to a hand injury suffered during Game 2 of the American League Division Series against the Minnesota Twins.