In this paper, a phase field model is developed for vesicle adhesion involving complex substrate and vesicle geometries. The model takes into account an adhesion potential that depends on the distance of vesicle to the substrate. A variational problem is solved in a 3D computational domain by minimizing the contribution of bending elastic energy and the adhesion energy under the constraints of total surface area and volume, described via a phase function. An adaptive finite element method is used to efficiently compute the numerical solutions of the model. The computational results are validated through comparison of several axisymmetric shapes with the sharp-interface ODE solution. Moreover, we compute shapes for non-axisymmetric situations to support the observation that concave substrates favor adhesion. © 2009 Elsevier Inc. All rights reserved.