Noises in the joints (popping, cracking or clicking) can be quite disturbing and cause concern. Often, these noises are not indicative of any underlying problem. Such noise often persists for years without any real problem developing. If there is no pain with these noises, you can assume it is being caused by the soft tissue in a joint and is normal. But noises associated with pain may indicate damage to the surfaces of the joint.
Cracking and clicking noises may be due to tears in the labrum, which may snap over the other structures as the arm moves. If the labral tear is at the top of the shoulder, it is called a "SLAP lesion". Sometimes the clicking may be due to the shoulder slipping in and out of joint. This is known as "shoulder instability". Other times an unstable long head of biceps may also dislocate out of its normal anatomic position, causing clicking/popping. This often needs further management.
A good clinical examination by an experienced clinician is the best way to make the diagnosis, with scans to assist when required. An MR Arthrogram is often useful to show a labral tear and is about 80 to 90 per cent accurate
If you have painful clicking and clunking, with a confirmed labral tear, keyhole surgery to repair the tear is the best treatment. If there is no labral tear, physiotherapy is best to retrain the muscles to control your shoulder.