Bicycle Mechanics - Clicking when pedalling

I had squeaky chain and fixed that with chain lube, now I can hear another noise but only when I pedal. It makes a click-clack sound every revolution of the pedals. It either goes away, gets quietier or I get used to the sound as the ride goes along. I'm not sure what would cause this? Maybe ball bearings in the crank hub? Anyone have any ideas what this could be?

Thanks

Could be
a) Pedals. They have bearings, so first try cleaning and lubing. You can also unclip one foot and see what happens as you pedal.
b)Bottom Bracket
c) Crank could have crack in it, I had similar sound issue which resulted in it cracking off mid- pedaling.
Oh yeah, I did try a & b first.

Another thing to check is for bent teeth in your chainrings. This got me once,
could not figure out the source of the sound until I found one tooth in each
ring bent slightly inward. The clicking was the sound of the chain snapping
back over the next (straight) tooth after the bent one in each revolution.

Could also be seat/seatpost or bar/stem.

If clicking there when standing and pedaling it is not the seat, otherwise, it is a candidate.

To remove chain/cassette/rings from the equation, noise would likely happen in synch with particular position of chain or ring/cassette. If noise more in synch with cadence, then likely not chain/ring/cassette.

I say likely because tracking down noises is not the easiest thing to do. Elimination methods can help narrow the search but are not perfect.

Could also be a mis-adjusted front derailleur. The crank could be hitting the derailleur cage. Does it happen in the big ring only?

Do you have a kickstand on your bike? Check if the crank is hitting the kickstand.

#1 cause though is usually the bottom bracket. Remove the BB and wrap the threads with Teflon tape and reinstall.

Put a lot of strain on your saddle, too. Grab it and bend it back and forth. See if you get the noise. That's probably the #2 cause I see in the shop.

Do your shoelaces have little plastic end-pieces on them? That can do it!

Is your chain old? Or too long?

Have you tightened every bolt down to the suggested torque-settings?

Have you read through this? :

http://sheldonbrown.com/creaks.html

Here are a couple of noises that took me awhile to track down:

1) The end of the cable for the front derailleur was sticking out just far enough to touch the drive-side crank lightly on each revolution. Bending the cable end slightly upward solved that problem.

2) The freewheel body was worn out so that it wobbled very slightly when pedaling under load (especially uphill). The noise sounded like it was coming from the pedals or bottom bracket, making it difficult at first to localize the sound. A new freewheel solved that problem.