We have investigated molecular distributions in protoplanetary disks, adopting a disk model with a temperature gradient in the vertical direction. The model produces suciently high abundances of gaseous CO and HCO + to account for line observations of T Tauri stars using a sticking probability of unity and without assuming any non-thermal desorption. In regions of radius R > 10 AU, with which we are concerned, the temperature increases with increasing height from the midplane. In a warm intermediate layer, there are signicant amounts of gaseous molecules owing to thermal desorption and ecient shielding of ultraviolet radiation by the flared disk. The column densities of HCN, CN, CS, H2CO, HNC and HCO + obtained from our model are in good agreement with the observations of DM Tau, but are smaller than those of LkCa15. Molecular line proles from our disk models are calculated using a 2-dimensional non-local-thermal-equilibrium (NLTE) molecular-line radiative transfer code for a direct comparison with observations. Deuterated species are included in our chemical model. The molecular D/H ratios in the model are in reasonable agreement with those observed in protoplanetary disks.