Start by discussing your standards. If your roommate is an Oscar and you are a Felix, you both need to compromise your standards and end up somewhere between squalor and a haven for obsessive compulsive disorder.
Make a list of chores and specify how often each needs to be done. Before you start divvying up the duties, brainstorm everything you can think of. Besides cleaning responsibilities, talk about who's going to shop for household necessities and food, if you share meals. The more detailed this list, the less chance of a problem later.
Assign who does what and when. There are many different kinds of agreements you can make, depending on who's involved. You might each pick tasks and stick to them for the duration of the lease, or you could switch off by week. Be flexible at this stage. If your roommate is really grossed out by a particular chore, volunteer to take it yourself and vice versa.
Decide how you're going to stick to the agreement. It's easy to figure out who's doing their part if you decide on a specific chore day. Either your roommate is there to help, or not. If not, talk about how long a chore can remain unfinished before there are consequences, and what the penalty would be.
Put it in writing. If you are rotating, make a chart. If you choose specific chores, write out an agreement and sign it. Should there be problems later, you'll appreciate that you have hard documentation.