If it is a short series of clicks (a 'tick, tick, tick' sound) this is fairly common. The click sound is caused by the drive parking its head. There are multiple causes for this, including power management and shock detection. If it is harmless, it will tend to happen when the HDD is idle.
If it is a louder knocking sound... You are more likely to have a problem.
Whichever the case, don't be complacent.... Download a copy of 'SMART reporter' (it's free) which will warn you of impending HDD failure in many cases. Also make sure that you keep everything backed up.
I might also be worth considering replacing your HDD as others have suggested, just to be safe.