Due to the fabrication processes, inaccurate manufacturing of the photonic crystals (PCs) might occur which affect their performance. In this paper, we examine the effects of tolerance variations of the radii of the rods and the permittivity of the material of the two-dimensional PCs on their performance. The presented stochastic analysis relies on plane wave expansion method and Mote Carlo simulations. We focus on two structures, namely Si-Rods PCs and Air-Holes PCs. Numerical results show—for both structures—that uncertainties in the dimensions of the PCs have higher impact on its photonic