The recognition of foreign molecules by the canine immune system and mounting a protective response to viral, bacterial, and parasitic pathogens requires intricate crosstalk between different immune cells and molecules, and inappropriate activation of these pathways can lead to allergic inflammation. The health of our canine companions is of great intrinsic value and dogs serve as a unique model for the study of naturally occurring complex diseases, such as allergies, and the study of host-pathogen interactions. In these studies, we examined the immune mechanisms associated with two canine diseases of major relevance in clinical practice - canine atopic dermatitis and canine parvovirus infection. Canine atopic dermatitis (CAD). To study the role of important immune cell types associated with excessive type 2 inflammation in allergic disease, we used new methods to describe a previously uncharacterized canine group 2 innate lymphoid cell-like (ILC2-like) population and canine T helper 2 (Th2) cells that express the transcription factor Gata3 and produce type 2 cytokines. We found that increased Th2 cells in the peripheral blood, but not ILC2-like cells, were associated with canine atopic dermatitis. Using single-cell RNA sequencing, we could show a unique gene expression signature in T cells from allergic dogs. Canine parvovirus (CPV) infection. To study the canine antibody repertoire to CPV, we developed new methods for the isolation of antigen-specific B cells and the cloning of CPV-specific monoclonal antibodies directly from dogs. We identified a vaccine-induced canine anti-CPV antibody that bound to an epitope on the capsid that includes the critical antigenic, receptor-binding and host-range residue VP2 300. We also cloned and expressed anti-CPV scFvs previously developed by others and established methods for isolating polyclonal antibody Fab fragments from dog blood. Cryo-EM analysis by members of Dr. Susan Hafenstein’s laboratory at Penn State University of the scFv:capsid and Fab:capsid complexes showed that canine-derived antibodies target two common antigenic sites on the parvovirus capsid, and that many canine antibody binding sites overlap the capsid region that binds to the host cell receptor, the transferrin-receptor type-1. The results in this dissertation highlight the importance of Th2 cells in chronic CAD, and also shed light on the canine antibody repertoire to CPV and the complex interactions between viral capsid structures, ligand binding, and natural variation.