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The information about the chemical compositions of stars is encoded in their spectra. Accurate determinations of these compositions are crucial for our understanding of stellar nucleosynthesis and Galactic chemical evolution. The determination of elemental abundances in stars requires models for the stellar atmospheres and the processes of line formation. Nearly all spectroscopic analyses of late-type stars carried out today are based on one-dimensional (1D), hydrostatic model atmospheres and on the assumption of local thermodynamic equilibrium (LTE). This approach can lead to large systematic errors in the predicted stellar atmospheric structures and line-strengths, and, hence, in the derived stellar abundances. In this thesis, examples of departures from LTE and from hydrostatic equilibrium are explored. The effects of background line opacities (line-blocking) due to atomic lines on the statistical equilibrium of Fe are investigated in late-type stars. Accounting for this line opacity is important at solar metallicity, where line-blocking significantly reduces the rates of radiatively induced ionizations of Fe. On the contrary, the effects of line-blocking in metal-poor stars are insignificant. In metal-poor stars, the dominant uncertainty in the statistical equilibrium of Fe is the treatment of inelastic H+Fe collisions. Substantial departures of Fe abundances from LTE are found at low metallicities: about 0.3 dex with efficient H+Fe collisions and about 0.5 dex without. The impact of three-dimensional (3D) hydrodynamical model atmospheres on line formation in red giant stars is also investigated. Inhomogeneities and correlated velocity fields in 3D models and differences between the mean 3D stratifications and corresponding 1D model atmospheres can significantly affect the predicted line strengths and derived abundances, in particular at very low metallicities. In LTE, the differences between 3D and 1D abundances of C, N, and O derived from CH, NH, and OH weak low-excitation lines are in the range -0.5 dex to -1.0 dex at [Fe/H]=-3. Large negative corrections (about -0.8 dex) are also found in LTE for weak low-excitation neutral Fe lines. We also investigate the impact of 3D hydrodynamical model stellar atmospheres on the determination of elemental abundances in the carbon-rich, hyper iron-poor stars HE 0107-5240 and HE 1327-2326. The lower temperatures of the line-forming regions of the 3D models compared with 1D models cause changes in the predicted spectral line strengths. In particular we find the 3D abundances of C, N, and O to be lower by about -0.8 dex (or more) than estimated from a 1D analysis. The 3D abundance of Fe is decreased but only by -0.2 dex. Departures from LTE for Fe might actually be very large for these stars and dominate over the effects due to granulation.