When the windows are down, the battery is being effected.

[dejs27]

When I shut off my 1999 4runner with the windows down and come back to it a couple hours later, my battery is dead. Yet when they are up there is never a problem. Anyone know why and how to fix it?

 

[Fourty-four]

When I shut off my 1999 4runner with the windows down and come back to it a couple hours later, my battery is dead. Yet when they are up there is never a problem. Anyone know why and how to fix it?

That sounds weird. If the windows are truly causing this, try to isolate the problem to one specific window. Then you can easily check to see if the window motor has a short.

Or another easy way to check is to use an ammeter to check your amperage draw. Just disconnect your battery cable and put your ammeter in series between the cable and the battery terminal. This will tell you the current draw on the battery with the ignition off. Test with the windows up and down.

 

[duzuck]

To add on to fourty-four's comment, anything over 50mA on the ammeter is bad. If testing the different windows doesn't help, try the ammeter test and pull fuses until the parasitic draw is back below 50. Right now, my 97 sits at about 26mA when turned off.