Background/Aim: Urine cytology is widely used for diagnosing urothelial carcinoma. However, it has limited sensitivity, particularly in upper tract urothelial carcinoma. The UF-5000 automated urine analyzer includes the research parameter Atyp.C, which quantifies cells with a high nuclear-to-cytoplasmic ratio. Although it has been utilized in bladder cancer, its application has not been evaluated in upper tract urothelial carcinoma. This study compared the diagnostic performance of urine cytology versus Atyp.C and assessed the advantage of combining them. Patients and Methods: This retrospective study included 41 patients with pathologically confirmed upper tract urothelial carcinoma without concomitant bladder cancer, as confirmed via cystoscopy. The sensitivities of urine cytology (Class ≥III), Atyp.C (≥0.1), and their combined use were compared. Results: Positive findings on urine cytology were detected in 11/41 patients (26.8%) and Atyp.C was observed in 9/41 (22.0%). When either test yielded a positive result, the detection rate increased to 17/41 (41.5%). A paired comparison using McNemar’s test demonstrated that the combined cytology-Atyp.C approach detected significantly more upper tract urothelial carcinoma cases than urine cytology alone (6 vs. 0 discordant pairs, p=0.041). Conclusion: The sensitivity of Atyp.C was similar to that of urine cytology. Some patients without hydronephrosis presented with Atyp.C positivity. However, this finding may be overlooked in routine clinical practice. Although its performance is lower than that reported in bladder cancer, Atyp.C is non-invasive and does not require additional procedures. Hence, it can be clinically useful for upper tract urothelial carcinoma diagnosis. Nevertheless, to validate this notion, prospective studies should be conducted.