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I did a search for this and could not find any reference to it. This information came from a Toyota TSB dated November 9, 2007 (TSB#EL009-07) I just added a remote to my 07 FJ and can confirm this information is accurate.

Begin With;
- Driver's door open and unlocked
- Key out of ignition
1. Insert and remove the key from the ignition switch 2 times within 5 seconds

NOTE: Steps 2 and 3 should be performed within 40 seconds

2. Close and open the driver's door TWICE.

3. Insert the key into the ignition and remove it.

NOTE: Steps 4-6 should be performed within 40 seconds

4. Close and open the driver's door TWICE

5. Insert the key into the ingnition

6. Close the door

7. Turn the ignition switch from "LOCK" to "ON" and back to "LOCK" at about 1 second intervals to select the desired mode from the list below:
- 1 time for ADD mode
- 2 times for REWRITE mode
- 3 times for CONFIRMATION mode
- 5 times for PROHIBITION mode

8. Remove the key from the ignition

9. To confirm your mode selection, the power locks will now cycle "lock" to "unlock" a number of times corresponding to your key cycles in step 7.

NOTE: If CONFIRMATION or PROHIBITION modes have been selected, opening the door will complete the procedure.

10. For ADD or REWRITE modes, do the following within 40 seconds of Door Lock confirmation;
A - Press both transmitter LOCK and UNLOCK buttons simulataneously between 1 and 1.5 seconds and release. (I had to do this a few times because I held the buttons down longer than the 1-1.5 seconds)
B - Within 3 seconds of step A, press the transmitter LOCK button from more than 1 second and release.
> If the transmitter has been successfully programmed, the power locks will cycle "lock" to "unlock" once at this time.
> If there are problems with the transmitter or the procedure up to this point, the locks will cycle twice. If this occurs, verify that you have received the correct transmitter, and then repeat the above procedure.
C - If multiple remotes are to be reprgrammed, repeat steps A and B

11. Open to driver's door to conclude programming mode

12. If you make an error during the programming mode, turn the ignition key to "ON" and back to "LOCK" to erase entered steps.

Good luck and ping me if you have any questions or issues. This procedure works for all 2007 and 2008 FJs as well as the following;

2000 - 2005 Celica
2001 - 2003 Prius
2001 - 2005 ECHO
2001 - 2007 Highlander
2001 - 2008 RAV4
2002 - 2006 Camry
2003 - 2008 Avalon, Corolla and Matrix
2004 - 2008 Sienna and Solara
2005 - 2008 Tacoma
2007 - 2008 FJ Cruiser and Yaris
I only have the valet key, will this procedure work with it?
 

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If my truck does not go into programming mode? What is the first thing to troubleshoot.
I have confirmed with Toyota that I do have Keyless entry.
What are the most common mistakes.
Thanks in advance.
 

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Can new key be programmed to start the car?
On my 2008 I was able to program a key without a fob attached using the above procedure. I haven't found a way to get the keys with a fob to program to start the rig but can get the fob programed to work the door locks.
 
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