First-principles molecular dynamics simulations are carried out to study the structural properties of liquid GeSe2. We use a generalized gradient approximation for the exchange and correlation energy, which we find to improve significantly upon the local density approximation in describing both the short- and the intermediate-range structure. A very good agreement with experiment is obtained for the total neutron structure factor over the entire range of momentum transfer. In particular, the first sharp diffraction peak (FSDP) is well reproduced. We carry out a detailed comparison between partial structure factors and partial pair correlations in theory and experiment to assess the quality of our simulation model. The short-range and intermediate-range structure are well described overall. However, residual differences between theory and experiment, such as the absence of a FSDP in the concentration-concentration structure factor, appear and are traced back to the Ge-Ge correlations. An analysis of the bonding configurations indicates that liquid GeSe2 is a defective network consisting of predominant Ge-centered tetrahedral units, but Ge- and Se-centered triads and homopolar bonds occur in non-negligible amounts. The number of Ge-Ge homopolar bonds and of ordered fourfold rings compare favorably with experimental estimates. Chemical disorder manifests through an important percentage of Se-rich odd-membered rings. We characterized the intermediate-range order by studying the relation between real-space distances and the FSDP. We found that this feature appears when correlations beyond 5 Angstrom are accounted for. The evaluation of bond lifetimes reflect the higher stability of Ge-Se bonds with respect to homopolar bonds, consistent with the predominance of tetrahedral units.