Martínez was signed by the Cleveland Indians as an amateur free agent in 1996. After a pair of minor league MVP awards and batting titles in 2001-02, he made his debut with Cleveland at the end of 2002.

In 2003, Martínez was busiest between Triple-A Buffalo Bisons and the Indians. He finished with a combined .315 batting average, hitting at a .349 clip in August and September with the big club. Exhibiting knowledge of the strike zone and an ability to make contact, he reduced his strikeout totals and produced a combined .376 on base percentage. He also drove in 63 runs, hitting .323 with runners in scoring position, and was selected to participate in the All-Star Futures Game played at Chicago's U.S. Cellular Field. From 2001-03, the Venezuelan slugger batted a combined .330 with 40 home runs and 194 RBI.

Showing defensive improvement, Martínez displayed an ability to call games at the major league level and began 2004 as the Indians' No. 1 catcher. In his first full-season he did a fine job defensively, hit .283 with 23 home runs, set a new record for Indians catchers with 108 RBI, earned his first All-Star selection, and shared the Silver Slugger honor as the top-hitting American League catcher with Iván Rodríguez. For the first time since the awards began in 1980, there was a tie at one position. On July 16, Martínez also had the best offensive night by a Tribe catcher in franchise history, when he hit three home runs, singled twice, drew a walk, and drove in a career-high seven runs in a perfect 5-for-5 game.

In June 2005, Martínez was batting .207 but he came into the season's final weekend batting .382 (96-for-251) after the All-Star break, the most for any ML player. He finished the season with a .305 average, 20 home runs and 80 RBI.