Prior to playing professional baseball, Denker attended Brea Olinda High School. Originally drafted by the Los Angeles Dodgers in the 21st round of the 2003 Major League Baseball Draft, Denker signed and started his professional career that very same year. He split time between the South Georgia Waves and GCL Dodgers, combining to hit .264 with three home runs and 14 RBI in 46 games.
Denker spent the entire 2004 season with the Ogden Raptors, with whom he hit .311 with 12 home runs and 43 RBI in 57 games. In 2005, he split time between the Columbus Catfish and Vero Beach Dodgers, combining to hit .281 with 23 home runs and 77 RBI in 132 games. He split time again between the two teams in 2006, hitting .247 with 16 home runs and 70 RBI in 129 games. He also walked 89 times and struck out 73 times.
He spent most of the 2007 season with the Inland Empire 66ers, until the Dodgers traded him to the Giants on August 25, 2007, as the PTBNL from the earlier trade for Mark Sweeney on August 9, 2007. Denker finished the season playing for the Giants Single-A Advanced team, the San Jose Giants. For the year, Denker hit .300 with 11 home runs and 66 RBI in 118 games.
Denker has hit .280 with 65 home runs and 270 RBI in 482 minor league games overall.
Denker got called up on May 12, 2008, and got his first major league hit against the Florida Marlins on May 25, 2008, which was a double down the third base line. He hit his first home run against Scott Schoeneweis of the New York Mets on June 3, 2008. Denker got sent down in June for Ivan Ochoa, who is another middle infielder.