The microscopic structure of temperature-sensitive polymer gels consisting of poly(N-isopropylacrylamide) (PNIPA) has been investigated in terms of small-angle neutron scattering. The spatial inhomogeneities, characteristic of polymer gels, in the PNIPA gels were evaluated as a function of the gel preparation temperature, T-prep, as well as the cross-link concentration, C-x. It was found that the spatial inhomogeneities increase with increasing T-prep or C-x. The effects of T-prep and C-x on the gel structure were successfully separated by a quantitative analysis of the structure factor with the Panyukov-Rabin theory. The effective degree of polymerization between cross-links, N, exhibited the opposite dependence with respect to T-prep and C-x. N was found to decrease with increasing C-x, while it increased with increasing T-prep. The temperature dependence of the Flory interaction parameter and the presence of the cross-link saturation threshold are also addressed with a discussion of the physical implication of these parameters.