1999 vw beetle how to program key remote

SOURCE: VW new Beetle

OK, it sounds like the battery is dead flat, or just dead. First thing to check is the voltage on the battery - if it is 12 to 13v it might just need recharging, but if it is a lot less it could be due for replacement.
You should be able to get it running by getting it jump started using cables from another car. When you get the engine running again check that no interior lights stay on after you close the door, and that no audio systems or other electrical items have been left on.

If the battery is more than three years old, it is probably just worn out, but if it is a lot newer, come back with more info and I will try to help you further.

I take it you have a "real" key to get you inside so you can open the hood / bonnet?

Hope this helps a bit to start with. D.

SOURCE: how do you change battery in key fob on 2002 vw golf

No problem. The key fob is two pieces. The key part and the remote. Open the key as you would to sue it. Where the key flips open you can see a small recess about where the line of the trunck switch. This is where the key separates. You can pull it off or pry it with a small screwdriver. Once separated with remote part in your hand this also splits in 2. In the same area you split the key off insert the screwdriver in this recess and the fob will open giving you access to the battery. Also can be done by hand. It is a little tight so you will have to force which is normal. No screws just clipped. Make sure the battery is positioned in the right way and that you have 3 volts when you test the battery. 2.7 volts will make the remote not work or act funny.

SOURCE: key fell out of remote fob 1999 vw beetle, bought used, one key

you have to go to the dealer and they can issue a new one....

SOURCE: 2001 VW Beetle Remote Key Battery

pull the top half off by hand . its hard but u can do it . then split buttom part in half by hand 3v battery

SOURCE: VW 2000 New Beetle door sensor/car alarm goes off when doors open.

I found a thread - http://forums.vwvortex.com/zerothread?id=1542461 that details the repair of the soldering on the key lock door module. Our 2000 new beetle had the same issue. Also sometimes it refused to start. Soldering pins fixed it all.

Also see http://forums.vwvortex.com/zerothread?id=1015107 for releasing window from track, And door handle from inner panel.

I ripped the door apart and re-solderd the pins. I only had one pin with cracked solder but two others looked thin so I did them while I was in there. It's about a four or five hour project if you have all the tools. (8mm triple square also called an 8mm internal was the hardest to find - Also needed Torx T8 T10 T15 and T30 plus Philips Screw Driver. )
Project is difficult but not too bad for the mechanically inclined. A 7 on a scale of 10.
Since re-soldering pins - no more issues! My guess is that a VW dealer would get $200 for a new moduel plus 5 hours of service time for this gig - easily a $500 to $1000 bill. My cost - several new tools - about $25.00.