  Direct measurements of cosmic ray (CR) species combined with observations of
their associated gamma-ray emissions can be used to constrain models of CR
propagation, trace the structure of the Galaxy, and search for signatures of
new physics. The spatial density distribution of the interstellar gas is a
vital element for all these studies. So far models have employed the 2D
cylindrically symmetric geometry, but their accuracy is well behind that of the
available data. In this paper, 3D spatial density models for the neutral and
molecular hydrogen are constructed based on empirical model fitting to gas
line-survey data. The developed density models incorporate spiral arms and
account for the warping of the disk, and the increasing gas scale height with
radial distance from the Galactic center. They are employed together with the
GALPROP CR propagation code to investigate how the new 3D gas models affect
calculations of CR propagation and high-energy gamma-ray intensity maps. The
calculations made reveal non-trivial features that are directly related to the
new gas models. The best-fit values for propagation model parameters employing
3D gas models are presented and they differ significantly from the values
derived with the 2D gas density models that have been widely used. The
combination of 3D CR and gas density models provide a more realistic basis for
the interpretation of non-thermal emissions from the Galaxy.
