In this paper I describe some of the recent advances made in the modelling of chemistry of protoplanetary disks, and in particular, of the inner regions where $r<100$ AU. These advances include the treatment of mass-transport processes, the interaction of radiation with chemistry, the augmentation of chemical networks to include isotopic species and their fractionation, and the attempt to connect disk chemistry with solar system bodies like comets. In the spirit of the title of this volume, I also briefly describe what in my opinion are the current challenges facing models of disk chemistry. These include the unification of chemistry, radiation and dynamics, the treatment of gas-grain interaction and the usefulness of observations to discriminate the different models in the literature.