Key fob on my audi a3 1998 has stopped working

would imagine you need to change the battery in the fob, when you put the key in the car after opening its regenerating the setting in the key, but losing it overnight because of depleted battery, do not know what you have in yours but they are normally a small coin type battery like this
CR2032 3v Lithium coin cell camera Battery Fujitsu

more than likely as the fob key has a chip that syncs with the security system etc , have you got the owners handbook as this should give you the procedure that needs to be carried out to reset the fob key,can't take the credit for this fix as found it at an audi forum give it a try .
I learned a new trick tonight. I recently changed the battery in my key and it would no longer open the door locks. I just sat down and read the manual and found that if you replace the battery you need to re-synch the key.

Here is how it's done.

replace the battery. ( pry open the little tab at the seam in the key, then split the bottom in two with your finger)

Press the lock or unlock button once.
with-in one minute put the key into the drivers door and lock and unlock it manualy.

TADA it works again

I have seen a few threads and questions that said there fob stopped working. so I thought I would throw this out there. I hope that some of you with this problem that don't have manuals because the previous owner kept it for a souvenir will find this Helpful.

Your KEY will not unlock the Door? That has nothing to do with the FOB.

OR do you mean your FOB will not work at all?. If it is a PROGRAMMING ISSUE, you need to contact your Dealer

hi you can do this but you will have to have a key that does not have a remote/fob on it ( basically just go get one cut cheaply ) then to reprogram keys/key fob's first using the key without fob, turn ignition on ( do not turn over, just to position 2) then lock drivers door with other key ( do not use fob, just the key itself with fob now complete the following within 30 seconds within 5 seconds( of locking the car) press the unlock button on the first key once ( this programs that key as key memory1) the indicators should flash once to indicate signal received wait 5 seconds then press unlock on key fob vehicle should then unlock meaning key fob has been programmed and programming ended open door turn ignition off , and that's it, it should work if you have more than 1 key with fob, do the same as above but instead of pressing unlock once, you do it twice, if third key 3 x if fourth key 4 x etc etc,

will your passenger door open with the key and is it just one side that your windows are not working or both. if its just one side it might be your regulator motor in the door thats not working if its both it might be your central locking pump usually in the boot. however if both of them are working fine it could be that your key needs reprogrammed however i think the 1st 2 are more likely to be the problem.

i have a rover 25 and the key fob is not opening the car i could use the key to open it but the alarm will go off and cant stop it without the fob...

I have an A4 and did this to re-program my key:

1. used the key to start the car...then turned it off
2. put the key in the driver door (door closed)
3. pressed the lock button on the key fob once
4. turned the key to lock the door.

This is basically the steps in the owners manual, but the car must be started with the key first, and the key must be in the door lock before pressing the lock button.

get in your car close door hit the unlock button then put key in the ignition cycle the key from off to on (STOP BEFORE START POSITION) cycle key off to on 7 times after the 7th trime the doors should lock the unlock automatically that means u are in trainning mode hit the unlock button on key fob. the key fob should now work if it doesn't then try changing batt

you may also have shorted the keyfob battery if you touched the front and back at the same time.joe