If you google scrotal masses the Mayo Clinic has some good information on causes.
You can also try the Urology forum here at Med Help. An ultrasound needs to be done to determine if it is a cyst or something else. Ask your sons doctor lots of questions so you can put any worries to rest. Hope your little guy is doing well.
my son is two years old. what is a cyst cause prom
You didn't mention how old your son is but I believe unless it becomes very large its left alone. I would think it would be important to monitor any growth and keep your sons doctor in the loop as far as any pain or unusual changes. Cysts can either be drained or surgically removed if necessary.