Background and Aim: Cytology investigations are a frequent part of ophthalmological examination. We aimed to assess whether the cytological findings of healthy and conjunctivitis/keratoconjunctivitis samples differed based on the evaluator's experience. Materials and Methods: A study evaluated healthy eyes (n = 40) and eyes affected with keratoconjunctivitis and/ or conjunctivitis (n = 28) in dogs. An ophthalmological examination was performed before sampling the eyes using a sterile cotton swab. An evaluator with theoretical experience and one with undergone clinical pathology residency training performed cytology blinded to the clinical findings. Results: In the healthy eyes group, the agreement between the evaluators for cellularity was nonexistent, while that for cell preservation and mucus content was fair. In the affected eyes group, the agreement for cellularity and mucus content was moderate, while that for cell preservation was fair. The inadequate sample rate differed significantly between the two evaluators in the healthy eyes group (p = 0.006) but not in the affected eyes group (p = 0.083). Bacterial presence was detected by both evaluators, and the findings did not differ statistically from the bacteriology results (p = 0.05). Significant variations were noted in the differential cell count; the mean count of the superficial epithelial cells and goblet cells of the healthy eyes group (p < 0.05) and that of the basal/intermediate cells and neutrophils of the affected eyes (p < 0.05) showed significant differences. Conclusion: The evaluator's experience significantly affected the differential cell count in both the healthy and affected eyes groups. Neutrophil degeneration was not observed by the less experienced evaluator, whereas bacteria were detected equally well by both the evaluators.