Bootsie is right, to a degree, women having cysts in their ovaries is a normal function of how the ovaries work (the egg is contained in a cyst for a while before it is released, and then the cyst usually becomes reabsorbed). However, there is a condition, called polycystic ovarian syndrome (pcos for short) that alters hormonal cycles and a number of other things. I'm suspecting, due to your irregularity of period, that this is what your doctor told you about.
It's a newer syndrome, so there isn't tons and tons of information on it, and it generally has much to do with your endocrine system (which is the system responsible for a whole slew of hormones). Most gyns that know enough about pcos suggest seeing an endocrinologist as they're the best able to treat it, but understand that it's so new a syndrome that exactly what needs to be done isn't absolute. Some doctors will prescribe birth control pills, (but that only regulates periods, it doesn't help with the other symptoms) while increasingly research is showing that using bcp or other related hormonal therapies only mask and in some cases exacerbate the disease. Pcos can affect your ability to have children, but then i've known of some women who have pcos who have, and are able to have, kids.
Truth be told there are still many doctors out there who really don't know a whole lot about pcos, so if one doctor doesn't seem to be up to snuff on it, then try to find another. And finding a good endocrinologist is a really good idea.
This website here:
www.Pcosupport.Org is a really awesome place to learn about it, and they do have a forum there with women who have it... A good place to read and learn. I do think they have a place with doctor recomendations, so you might want to check it out and see what doctors or other resources are available. I know of one pcos clinic, it's in pennsylvania, which may or may not help you.
Good luck.