A boundary integral equation for the eigenmode of photonic crystal fibers is formulated and numerically solved using the Nystrom method. The real and imaginary parts of the propagation constant, which are related to the dispersion and the confinement loss of fibers, are obtained using a secant method. This formulation is very flexible to handle the fiber geometry, and therefore can be applied to photonic crystal fibers with novel refractive index profile and hole geometry.