I have a 99 Honda civic ex manual. And it does not crank?

I have checked battery, starter, clutch safety switch, and put a new ignition switch and still dies not crank.

What about the alarm (Immobilizer) system? Have you checked into it? Any light blinking on the dash? When I read what you've typed:

"I have checked battery, starter, clutch safety switch, and put a new ignition switch and still dies not crank."

Which one is it? Not cranking or start, run then dies out? Have you checked the fuse #41 (80A) and #42 (40A)? Or the starter cut relay? These two fuses supplies the battery power to the ignition switch W/B wire (Hot at all time). The Civic may have wiring problem.

At the clutch safety switch, is there B+ at the BL/B wire? This BL/B wire get the power from the Starter cut relay, when this Starter cut relay energized (By depressing the clutch safety switch), it provides the power to the starter solenoid B/R wire.

So my question is: Do you have B+ at this B/R wire when the ignition switch is in the "Crank" position? It's a simple circuit. Do you have a wiring diagram for the starting system of 99 Civic Ex?

Go to this link, it contains most diagrams for the Civic, but diagram #9 would be what you'll need to look at:

http://www.autozone.com/...528018f8b2

But if you need the whole 99 Civix Ex ETM (Electrical Troubleshoot Manual) that come from Honda. Click on my sign on name and E mail me and I'll send it to you to down load. Other than that, diagram #9 is all you need to take care of the problem.

This video may help:

Happy hunting and if you need more help or have questions? E mail me. HTH