If the cyst isn't bothering you, one treatment option is to leave it alone. In half the cases, it will go away by itself. If it creates problems (pain or loss of wrist/hand function), then it can be aspirated or excised. Aspiration means a long, thin needle is inserted into the cyst and fluid is drawn out. Excision is the surgical removal of the cyst.
You should be aware that recurrence is high with aspiration. Even with removal, ganglion cysts often come back but the recurrence rate is much lower. Hand surgeons are now investigating the use of an open incision versus arthroscopic surgery to remove ganglion cysts. They are particularly interested in whether the recurrence rate is different between the two surgical techniques.
A study was recently published comparing recurrence rates for these two surgical approaches. No difference was found in rates of post-operative residual pain or recurrence. More studies are needed to provide surgeons with the information they need about outcomes with various approaches to this problem.
Most experts agree with the wait-and-see approach suggested by your physician. If the cyst grows or causes further problems, aspiration or excision is always available.