BACKGROUND: Urinary tract (UT) cytology has been used successfully to diagnose high-grade urothelial carcinoma but is reported to have poor sensitivity for low-grade urothelial neoplasms (LGUNs). However, the literature has shown thatLGUN may be associated with atypical findings in UT specimens. The authors determined which features were most commonly observed, and whether the method of specimen procurement had an effect. METHODS: A total of 326 specimens were identified over an 8-year period. One hundred fifty-three specimens were reviewed and graded for cellularity, number of tissue fragments (TFs), degeneration, inflammation, hyperchromasia, nuclear pleomorphism, nuclear border irregularity, nuclear size, cytoplasmic tails, nuclear eccentricity, and high-grade features. RESULTS: Of the 153 specimens, 86 specimens (56.2%) demonstrated cellular atypia; of those, 51.2% were voided urine (VU) and 31.4% were UT washing (UW) specimens. The majority of specimens had many cells (46.5%), many single cells (44.2%), few to moderate TFs (46.5% and 27.9%, respectively), mild hyperchromasia (52.3%), mild nuclear pleomorphism (51.2%), mild nuclear border irregularity (60.5%), cytoplasmic tails (51.2%), and few to moderate eccentric nuclei (37.2% and 36.1%, respectively). The presence of TFs, cytoplasmic tails, and eccentric and enlarged nuclei were significantly more common in UW versus VU specimens (P 5 .036, .012, .014, and .027, respectively) and in UW versus benign UW controls (P 5 .001, .002, .002, and .003, respectively). CONCLUSIONS: Approximately 50% of UT specimens with LGUN on follow-up demonstrated atypical features. Based on comparison with benign UW controls, TFs, cytoplasmic tails, nuclear eccentricity, and enlarged nuclei were more pronounced in neoplastic UW than VU specimens, suggesting that the method of urine specimen procurement affects the presence of certain low-grade features. Cancer Cytopathol 2016;124:552-64.