Wow. We really need more information here. What kind of drain are we talking about, sewer? Storm?
How old is the drain?
Does it have good slope?
PVC, Cast Iron, Clay Pipe? Something else?
There are some products you can pour down your drain cleanout to work on the roots, but if there are roots in your sewer, killing them once is not going to change the fact that you have open connections or outright cracks in your drain. Having to replace the drain outright is not an impossible solution either, depending upon your problem.
One good idea is not to plant trees around your sewer line, but it's too late for you on this point.
A good qualified plumber in your area would be able to scope out your drain and give you some qualified recommendations. He can actually send a video camera down the drain line to inspect for cracks, roots, slope, etc and give you a real good idea of what you're up against. This kind of consultation shouldn't cost a lot, maybe $50-75 (maybe more, been awhile since I've done it.)
I may be way off track here. Post back with more specifics if I am.