From the help of ode45:
For a scalar T and a vector Y, ODEFUN(T,Y) must return a column vector corresponding to f(t,y).
So what you ask for is not possible. You might have to live with a work-around where you stack your column-vectors, let's call them x and y, into a single column-vector xy. This should be "rather straightforward" when it comes to modifying your ODEFUN - you would only need to "unstack" them at the top of the function and then stack the respective derivatives (dx and dy) back together (dxy = [dx;dy]) and the ode-integration should work just fine. Then you'll have to handle having the two columns above each other instead of next-to once you get the solution, but that should be a trivial (but admittedly slightly annoying) step to take.
HTH
