The study of atypia in urinary cytology has been ongoing for decades but most studies have focused primarily on test performance in patients with concurrent biopsies and/or limited follow-up periods. While these data are useful, many studies fail to consider patient factors that may alter the pretest probability, which can subsequently affect test performance. An isolated diagnosis of malignancy in urinary cytology usually has a high positive predictive value and allows a urologist to conduct a rigorous workup of the patient to establish a tissue diagnosis. However, it is less certain how an atypical diagnosis impacts patient care, given that many patients have a history of bladder cancer and are already under surveillance with cystoscopy at regular screening intervals. Furthermore, a discrete negative urine cytology is unlikely to allow a patient to forego a cystoscopy procedure due to limitations in the sensitivity of urine cytology. Over the last several years, the introduction of The Paris System for Reporting Urinary Cytology (TPS) has improved the predictive value of atypical diagnoses, but additional studies are needed to evaluate the performance of these diagnoses in specific clinical situations. Such data could better inform urologists on how to manage patients with atypical diagnoses. This review discussed the diagnosis of atypia in urinary cytology and the impact of such a diagnosis in various clinical contexts.