Various cellular processes require the participation of specific anions, including Cl-, F-, I-, HCO3- and CO32-. However, their ionic charges impede their permeation across the hydrophobic lipid bilayers of the cells. Cell membranes thus contain specific macromolecular transport proteins, ion channels and transporters, to facilitate and control the passage of anions across the lipid bilayer. Anion-transport proteins need to be able to discriminate between different anions to carry out their function. What drives the protein selectivity for different substrates is a fundamental question that has long fascinated scientists. However, anion recognition in proteins is still poorly understood due to the lack of crystal structures of anion-transporting proteins and the underdevelopment of computational tools for studies of anions. To fill some of these gaps, this thesis elucidates important determinants of ion selectivity in proteins, involved in the transport of Cl-, I-, F-, HCO3-, and CO32- from several different protein families. In chapter 2, we studied carbonate and bicarbonate binding in proteins, through a survey of the preferred coordination numbers, amino acid and atom type composition of the coordination spheres of HCO3- and CO32- in bicarbonate- and carbonate-bound proteins deposited in the Protein DataBank. Some interesting differences in the coordination patterns for HCO3- and CO32- were highlighted. In chapter 3, we evaluated the thermodynamics of anion binding in a series of binding sites constructed from real anion-binding proteins using Quantum Mechanics calculations. The importance of the thermodynamics of binding for the anion selectivity was discussed. In chapters 4 and 5, we assessed the anion dynamics in proteins from the SLC4 and SLC5 families, respectively, using various computational methods, which led to the identification of putative binding sites in the protein matrix for sodium and the transported anions. Our work contributes to the increasing body of knowledge on anion-protein interactions and provides important mechanistic insights into the anion transport and selectivity of several proteins of interest for human physiology.