Atopic dermatitis is a chronic, pruritic inflammatory skin disease affecting approximately 10% of dogs worldwide. The disease typically manifests at an early age, causing pruritus and secondary skin lesions in specific anatomical regions. The pathophysiology of canine atopic dermatitis (CAD) remains incompletely understood, but recent research suggests a complex interplay between skin barrier dysfunction, allergic sensitisation, and microbial dysbiosis. Despite the well-established association between atopic dermatitis and conjunctivitis, the prevalence of conjunctivitis in dogs with CAD is often underestimated in clinical practice due to inadequate recognition of symptoms and a lack of specific diagnostic protocols. This study aimed to analyse the cytological characteristics of the conjunctiva in dogs affected by atopic dermatitis. Samples were collected from 24 dogs diagnosed with CAD and treated at the University Veterinary Hospital, Faculty of Veterinary Medicine, University of Zagreb. Cytological analysis was performed on samples obtained using a cytobrush. The results revealed the presence of inflammatory cells in all samples, with lymphocytes most prevalent (87.5%). A mild degree of conjunctival metaplasia was observed in all dogs, regardless of the type of inflammatory cells and the severity of conjunctivitis. These findings suggest that atopic dermatitis may induce changes in the conjunctiva that are not necessarily correlated with the intensity of the inflammatory response. The presence of lymphocytes, along with eosinophils in some cases, underscores the diagnostic value of conjunctival cytology in dogs with CAD. Furthermore, the increased density of goblet cells suggests similarities in the pathophysiology of ocular allergies in dogs and humans, opening avenues for further research to better understand and treat these conditions. This study highlights the importance of an interdisciplinary approach in the diagnosis and treatment of atopic dermatitis, including regular ophthalmologic examinations as part of standard clinical practice.