The innate immune system provides the immediate defense against pathogens. NOD1 and NOD2 proteins are intracytoplasmic signaling receptors of the innate immune system and recognize conserved microbial molecular structures. The aim of this study was to analyze the expression of NOD1 and NOD2 proteins in healthy mouse and dog eyes using immunohistochemistry on formalin-fixed, paraffin-embedded globes. In both the mouse and dog globes, a strong immunosignal for NOD1 and NOD2 was present within corneal epithelium, corneal endothelium and conjunctival epithelium. Scattered cells in the conjunctival substantia propria displayed moderate immunopositivity for NOD1 and NOD2. Additionally, in dog eyes, nonpigmented iridal epithelium was immunopositive for NOD1 and NOD2. No other examined ocular tissues were immunopositive for NOD1 or NOD2. To the best of the authors’ knowledge, this is the first description of an immunohistochemical study on NOD1 and NOD2 expression in healthy mouse and dog eyes. Since signaling molecules of the innate immune system mediate pro-inflammatory responses in numerous organs, they likely also contribute to the pathogenesis of ocular inflammation.