The authors construct Heegaard Floer theory for 3-manifolds with connected boundary. The theory associates to an oriented, parametrized two-manifold a differential graded algebra. For a three-manifold with parametrized boundary, the invariant comes in two different versions, one of which (type $D$) is a module over the algebra and the other of which (type $A$) is an $\mathcal A_\infty$ module.