last night at work I went out to my 2001 4runner (v6 auto)
battery (optima red only a few yrs old) was nearly dead and there was a loud click-click coming from battery area. not much light where I was parked so I couldnt see anything.
I thought what could be draining it? and unplugged my radar detector which is in lighter plug but doubt that really mattered.
when battery cables were hooked up, it immediately started alarm and lights came on fully bright.
truck started right up.
no problems this morning......

any hints?

 

Sounds like it might be an alarm issue.

Anything aftermarket you have installed?

 

First thing I'd check is your battery terminals. Make sure there is zero movement in them and that they're clean of any corrosion. Loose terminals, especially when it's a bit cooler at night, causing them to contract slightly, are a very common reason for a no-start.

Second thing I'd look for is something like DeathCougar suggested. If you don't have any aftermarket add-ons like that, take a look at things like the glovebox light which can cause a slow drain.

Third thing I'd check is the grounds.

 

the loud click click sound was happening with the hood open key out and me standing next to car. not when trying to start the truck. i guess i wasnt to clear on that.
nothing left on and no aftermarket stuff.
i think it is a relay
does the headlight relay make a sound like that? i usually drive with my lights on all the time since they shut off with the key

 

Was the noise continious?...I am not positive,but I think the evap purge valve can and will cycle with the key off..but it should only happen for less than 20seconds.

If its continious...start pulling fuses,untill the one you pull makes the noise stop.

You could always just have a dead/bad connection at battery,If the clicking is not continious.

If its not continious,do an amperage draw on the neg side..needs to stay at or under 50 milliamps..or its causing a drain on your battery....same deal with that..if over 50 milliamps..start pulling fuses to find the circuit thats causing the drain.

 

I had the same thing happen (I think). I accidentally drained the battery through a quark in the auto headlights which set off what you are talking about. In my case, I think when the battery was drained it set off the alarm system and due to the low voltage the relay was clicking as the alarm was attempting to go off. The clicking and the alarm LED on the dash were in sequence. The battery was so dead that I couldn't use the key fob to unlock the doors, I had to use the key. Once the battery was recharged I have not had a problem since.

The quark that set this off was as follows: I leave my headlights on all the time and they automatically turn off. Sometimes I use a small cigarette lighter air pump to check the pressure of my motorcycle tires. On the day that I killed the battery I opened the passenger side door (all other doors closed), reached across the seat and turned the ignition on (motor off) so that the power outlet in the front would have juice. I then filled the motorcycle tires, turned off the ignition and closed the door. If you do it in that sequence, the headlights will stay on. If you do in from the driver’s side door, they will go off. I guess Toyota didn't think of that situation, it seems to be controlled by the driver’s door. Twice I have had this happen, the second time I forgot about it and the battery died.

 

good post by heddleston above

short answer-do not rely on the auto shut off feature. Get in the habit of shutting your lights off at the switch when you turn off the vehicle.