We have studied the basis set and electron correlation effects on the ab initio calculations of two-photon absorption cross sections of water. Various series of correlation consistent basis sets up to triply augmented basis sets of valence pentuple zeta level as well as the popular 6-31G(d) basis set have been employed in combination with several coupled cluster, configuration interaction, and density functional theory methods. We find that it is very difficult to obtain converged values of the cross sections for even a small molecule such as water. Acknowledging these difficulties in obtaining a fully converged cross section for a given state, we also investigated the possibility of determining relative cross sections for a series of organic molecules. However, we did not find consistency between the relative cross sections calculated at the Hartree-Fock level and several coupled-cluster methods using the 6-31G(d) and aug-cc-pVDZ basis sets. However, we could reproduce the relative ordering of the two-photon absorption cross sections of the molecules studied at the Hartree-Fock level.