BackgroundNuclear protrusions such as micronuclei (MNs) and nuclear budding (NB) are morphological findings of chromosomal instability and indicators of genotoxic damage. They are increased in malignancies, and their high frequency may be used in the diagnosis of cancers and the follow‐up of patients. Urothelial carcinomas are common tumors that cause morbidity and mortality, and cytology is a commonly used method for the monitoring and screening of urothelial carcinoma. Although the cytological evaluation of urinary samples is mainly based on nuclear features, there is limited research focusing on MN frequency in urinary cytology. This study aimed to investigate MN and NB counts in various diagnostic categories of urinary samples.MethodsThis study included 117 urinary cytology samples categorized according to The Paris System for Reporting of Urinary Cytology. Two observers, blinded to the diagnosis, counted the frequency of MNs and NB per 1000 cells on May‐Grünwald‐Giemsa– and Papanicolaou‐stained slides.ResultsMN and NB counts significantly differed among the groups (p < .001 for each) with a large effect (Ɛ2 = 0.509). MN and NB counts were significantly higher in cases with high‐grade urothelial carcinoma (HGUC) than in control cases and in cases that were negative for HGUC or with atypical urothelial cells (p < .001 for each). Any MN count greater than 2.5 per 1000 cells indicated HGUC with a 55% sensitivity and 92.4% specificity.ConclusionsBecause increased MN and NB frequencies are closely associated with an increased risk of malignancy, these could be integrated into The Paris System for Reporting of Urinary Cytology.