This paper presents a Galerkin boundary element method for solving crack problems governed by potential theory in nonhomogeneous media. In the simple boundary element method, the nonhomogeneous problem is reduced to a homogeneous problem using variable transformation. Cracks in heat conduction problem in functionally graded materials are investigated. The thermal conductivity varies parabolically in one or more coordinates. A three dimensional boundary element implementation using the Galerkin approach is presented. A numerical example demonstrates the efficiency of the method. The result of the test example is in agreement with finite element simulation results.