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Background and Objectives: Urine serves as a vital diagnostic fluid, and urine cytology analysis plays a crucial role in identifying urinary system illnesses such as bladder cancer and kidney stones. The Paris System for Reporting Urinary Cytology establishes a uniform method for diagnosing urinary tract cancer. This study aimed to provide valuable insights that can inform diagnostic strategies related to kidney stones and ultimately improve patient outcomes via the early detection of the cellular changes associated with kidney stones and their relation to kidney function tests. Materials and Methods: A comparative study was conducted and comprised two groups: group 1, consisting of 50 patients diagnosed with kidney stones, and group 2, comprising 50 patients diagnosed with other kidney diseases. Renal function tests and urinalysis (via the PAP staining of urine cellular deposits to detect nuclear changes) were performed, and the results were analyzed. Results: There was a statistically significant increase in urinary red blood cells, white blood cells, and nuclear reactive atypical changes in urinary sediments of kidney stone patients compared to the patients without stones, while there was a decrease in the estimated glomerular filtration rate (eGFR). eGFR showed a 96.7% specificity in detecting cases with nuclear reactive atypia. Conclusions: eGFR emerges as a reliable diagnostic marker for the comprehensive assessment of kidney stones, particularly when associated with nuclear atypia. The significant correlation between the indicators of chronic kidney disease, such as decreased eGFR, and the presence of kidney stones emphasizes the urgent need for efficient diagnostic practices. [ABSTRACT FROM AUTHOR]