I have a 2001 Honda Civic 4 door it has a prestige remote start and keyless entry. The remote is a 4 button remote with 2 blue buttons for lock and unlock the doors in the bottom left is a green butto

The Lock's lock from the door switches ? If they do it's not a fuse problem . Which of these does your vehicle have ?
Keyless Entry System Description and Operation (with Accessory 2 Way Remote)
Keyless Entry System Description and Operation (without Accessory 2 Way remote)

The keyless entry system is a vehicle entry device. The keyless entry system is used in conjunction with the body control module (BCM) to remotely activate certain vehicle features. Keyless entry will lock/unlock the doors/liftgate when a corresponding button on the keyless entry transmitter is pressed. This is accomplished by the transmitter sending a radio frequency to the remote control door lock receiver (RCDLR). The RCDLR interprets the signal and activates the requested function via a serial data message to the BCM. A low transmitter or vehicle battery or radio frequency (RF) interference from aftermarket devices, such as 2-way radios, power inverters, computers, etc., may cause a system malfunction. High RF traffic areas may also cause interference that could lead to a malfunction. Keyless entry allows you to operate the following components:
• Door locks
• Liftgate lock
• Vehicle locator/Panic alarm
• Illuminated entry lamps
• Remote vehicle start
The keyless entry system has the following components:
• Keyless entry transmitters
• Keyless entry antenna
• 2 Way Advanced Remote Start RCDLR
• BCM

Your best bet , take it to a GM dealer .

Here are the instructions from the factory service manual:
1. Enter 5-digit permanent entry code into the keyless entry keypad.
2. Within 5 seconds of pressing last button of code, press the 1/2 button. All doors will lock then
unlock confirming you are in programming mode.
3. Press any button on first Keyless Remote within 5 seconds of pressing the 1/2 button. Locks will
cycle to indicate succesful programming.
4. If you are programming more than one Keyless Remote (Including any exsiting remotes) Press
any button on second keyless remote within 5 seconds of previous remote. Locks will cycle again
to indicate succesfull programming. (If the keypad light goes out before all remotes are
programmed the entire process must be repeated).
5. Press the 7/8 and the 9/0 buttons simultaneously on the keypad to exit program mode.

Hi.

To program ( or reprogram ) a keyless entry remote transmitter into the remote keyless entry module, perform the following steps:

1. Turn the key to ON or ACC and short the two terminals of the program connector, a two-pin connector located below the driver's side of the instrument panel at the base of the steering column. All doors should lock and then unlock.
2. Press any button on each keyless entry remote transmitter in turn. All doors should lock and then unlock. If the door locks do not respond, press the button again (up to three times maximum with the same keyless entry remote transmitter). If the door locks still fail to respond, go to Pinpoint Test A.
3. Repeat Step 2 to program additional keyless entry remote transmitters into the remote keyless entry module (up to four keyless entry remote transmitters maximum).
4. Turn key off.
5. Remove the short from the program connector. All doors should lock and then unlock.
6. Verify that the keyless entry remote transmitters have been successfully programmed by pressing the LOCK or UNLOCK button on each one, and observing that the system responds by locking and/or unlocking the doors.


I hope this helps you.

Thanks!

. Enter 5-digit permanent entry code into the keyless entry driver door keypad. 2. Within 5 seconds of pressing last button of code, press the 1/2 button. All doors will lock then
unlock confirming you are in programming mode.
3. Press any button on first Keyless Remote within 5 seconds of pressing the 1/2 button. Locks will
cycle to indicate succesful programming.
4. If you are programming more than one Keyless Remote (Including any exsiting remotes) Press
any button on second keyless remote within 5 seconds of previous remote. Locks will cycle again
to indicate succesfull programming. (If the keypad light goes out before all remotes are
programmed the entire process must be repeated).
5. Press the 7/8 and the 9/0 buttons simultaneously on the keypad to exit program mode.

SECTION 501-14B: Keyless Entry/Computer Operated Locks 1999 Town Car Workshop Manual GENERAL PROCEDURES Programming —Keyless Entry Keypad Code

1. Enter the permanent factory keyless entry keypad code.

1. Press the 1/2 button within five seconds to activate the programming mode. Holding the 1/2 button for more than two seconds will erase all stored customer codes. The existing codes do not need to be erased to program new codes.

1. Enter the new five-digit keyless entry keypad code.

1. To associate the new code with personality positions 1, 2 or 3, press the 1/2 button within 5 seconds of entering the 5th digit of the new code for position 1 or 3/4 button for position 2 or 5/6 for position 3. The door locks will lock and unlock confirming the new code is programmed.

1. If another code is to be programmed, begin entering the code within 5 seconds of the last button pressed.

1. After all new keyless entry codes are programmed:
   • Press keyless entry keypad buttons 7/8 and 9/0 at the same time to exit the program mode.
   • Wait for 5 seconds; the driver door module (DDM) will exit the program mode automatically.
   • -------------------------------------------------------------

Programming —Transmitter

1. Cycle the ignition from OFF to RUN four times within three seconds. The locks will then lock and unlock, confirming program mode has been entered.

1. NOTE: When the first keyless entry remote transmitter is programmed, all other keyless entry remote transmitters are erased.
   Press any button on the transmitter to be programmed.

1. If additional keyless entry remote transmitters are to be programmed, repeat step 2 within 7.5 seconds.

1. To exit program mode, turn the ignition to START or wait 7.5 seconds.

--------------------------------------------------
Programming —Remote Memory Activation NOTE: This procedure must be completed within 5 seconds.

1. Press the SET button on the driver door panel.

1. Press any button on the keyless entry remote transmitter to be associated with a memory setting.

1. Press the 1 or 2 memory button on the driver door panel.

-------------------------------------------------------------
Programming —Autolock and Horn Chirp

1. NOTE: This procedure must be completed within 30 seconds.
   Turn the ignition switch to RUN.

1. Press the UNLOCK button three times.

1. Turn the ignition switch to OFF.

1. Press the UNLOCK button three times.

1. Turn the ignition switch to RUN. The doors will lock and unlock to confirm entry into program mode.

1. Press the UNLOCK button once to toggle the Autolock feature on or off, or twice to toggle the Horn Chirp function on or off. The horn will chirp to confirm toggling of the Autolock feature.

1. Exit program mode by turning the ignition to OFF, START, or wait 7.5 seconds.

----------------------------------------------------------------------------------

does trunk button work? panic button?
here's 2003 info:

• The doors do not lock/unlock using the remote transmitter

• Remote transmitter.
• Driver door module (DDM).

• Go To Pinpoint Test G .

SECTION 501-14: Handles, Locks, Latches and Entry Systems 2003 Town Car Workshop Manual
GENERAL PROCEDURES Remote Transmitter Programming

1. Cycle the ignition from OFF to RUN four times within three seconds. The locks will then lock and unlock, confirming that the program mode has been entered.

1. NOTE: When the first keyless entry remote transmitter is programmed, all other keyless entry remote transmitters are erased.
   Press any button on the transmitter to be programmed.

1. If additional keyless entry remote transmitters are to be programmed, repeat Step 2 within 7.5 seconds.

1. To exit program mode, turn the ignition to START or wait 7.5 seconds.

--------------------------------------------------------------
report back

Okay, here goes-

1. Turn Key to on position.
2. Push and hold **valet button on the stock radio.
**Valet button is skinny bar located between am/fm & cd/tape buttons on stock radio.
Door locks will cycle one time.
3. Press any button on remote one time within 20 seconds. Door locks will cycle again.
4. To program up to 4 additional remotes repeat step 3 for each additonal remote.
5. Turn key off programming is complete.

Thanks for using Fixya, please rate if this helps :)

ok here is the porcedure that i have for it

Remember , these steps must be preformed within 5 seconds of eachother also all doors should be closed, radio and lights turned off

im not sure what you mean by a bypass, you can always just not use the remotes and go into the body control computer and turn off keyless entry

1) Unlock Doors
2) Turn ignition key to "ON" position (II)
3) Press the "LOCK" or "UNLOCK" button on the remote
4) Turn the ignition key to the "OFF" position (0, I)
5) Turn the ignition key to the "ON" position
6) Press lock or unlock
7) Turn key to off position
8) on position
9) lock or unlock
10) off position
11) on position
12)lock or unlock - doors should cycle to indicate successful programming. If you only have one remote, turn ignition to off or don't touch anything. if you have 2+ remotes, go to 13:
13) lock on each transmitter that you need to program

*Steps 2-12 must be performed within 5 seconds of each other. Step 13 can be performed within 10 seconds of step 12.

Hey .. i have a 99 civic also and i found my door doesnt lock unless u open the handel and then lock it and was talking to the shop and they told me things get gumed up inside and take it apart and clean it up with lub .. try that see if it works sounds like same problem

this maybe a long shot. but i feel that it could be your remote. the "chip" inside your remote could be weak in frequency.