One problem related to clutch pedal/linkage has been reported for the 2003 Honda Civic. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2003 Honda Civic based on all problems reported for the 2003 Civic.
Manual transmission clutch depressed all the way to the floor but shifting is not smooth and lots of times even "grind" into 2nd gear at low speed(disengage at about 3000rpm then shift into 2nd). Feels like the shifter tires to push back to neutral. Also clutch pedal does not release so smooth after a long period of driving, making noise when pushing down and "clicks" when engaging.