Cytological examination is routinely applied in clinical work because of its efficiency, speed and simplicity. Histological examination is more complex, it requires more time for specimen preparation, but it is the gold standard for analyzing tissue architecture. Both methods are performed by the Department of Veterinary Pathology Veterinary Faculty, University of Zagreb, but the rate of congruency between those methods has not yet been investigated. The Department archives were searched for all cases (pairs) that went through both cytological and histological examination of the same lesion, between 2009 and 2016. Altogether 251 cases were found and the majority were canine. Statistical analysis of accuracy and efficiency of cytological cases in relation to histological cases was conducted on 251 cases registered in the Department archives between January the 1st 2009 and January the 1st 2016. With indecisive (non-diagnostic) cases excluded (20,7%), the rate of complete or partial congruency between cytological and histological diagnosis was 80,4%, and the rate of non-congruency was 19,6%. Majority of samples were taken from the skin region (50,6%), where mastocytoma had the rate of 20,5%, as opposed to other lesions which combined had a rate of 79,5%. Results have shown 96,6% congruency in mastocytoma cases, regardless of the region. The results are similar to those obtained in comparable researches, either human or veterinary medicine. Research concerned has shown a great congruency rate between cytological and histological diagnosis and cytological examination was proven (complemented with histological examination) as very important and useful screening method in classification of skin lesions in domestic animals.