We present a method to calculate total X-ray scattering cross sections directly from ab initio electronic wave functions in atoms and molecules. The approach can be used in conjunction with multiconfigurational wave functions and exploits analytical integrals of Gaussian-type functions over the scattering operator, which leads to accurate and efficient calculations. The results are validated by comparison to experimental results and previous theory for the molecules H2 and CO2. Importantly, we find that the inelastic component of the total scattering varies strongly with molecular geometry. The method is appropriate for use in conjunction with quantum molecular dynamics simulations for the analysis of new ultrafast X-ray scattering experiments and to interpret accurate gas-phase scattering experiments.