Atomistic simulation techniques have been used to investigate the energetics of defects, oxygen migration and proton incorporation in the high temperature proton conductor LaYO3. The interatomic potentials have reproduced the observed unit cell parameters. Defect calculations indicate that Schottky-type defects have unfavourable energies of formation. The calculation of the energies of solution for alkaline-earth dopants revealed that Sr has the highest solubility in accord with experiment. It was estimated that oxygen migration takes place via a curved route with an activation energy of 1.22 eV. The enthalpies for the incorporation of water into alkaline earth doped LaYO3 were also calculated.