Background: Urinary stone disease (USD) refers to the presence of stones or salt crystals within the urinary tract, with calcium stones accounting for approximately 80% of cases. Increased urinary calcium and phosphorus excretion predispose individuals to urinary stones, with hypercalciuria being the most significant risk factor. Vitamin D plays a pivotal role in modifying urine calcium and phosphorus excretion, and it enhances calcium and phosphorus reabsorption in the kidneys. Urinary stone disease is a recognized risk factor for chronic kidney disease (CKD) and may also lead to life-threatening complications such as perinephric abscesses, urosepsis, and urinary tract malignancies. The role of serum vitamin D and its effects on serum calcium and phosphorus in urinary stone formation have been subjects of controversy. Objectives: This study aims to evaluate the associations between serum calcium, phosphorus, and vitamin D levels and urinary stones. Methods: This retrospective study involved two groups of 90 patients, one with urinary stones and the other without. Demographic and biochemical data, including serum calcium, phosphorus, and 25-(OH) vitamin D levels, were recorded for all patients. Patients were categorized into four groups based on their serum vitamin D levels: Excess, sufficient, insufficient, and deficient. The presence and characteristics of urinary stones were assessed using non-contrast CT scans. Results: The mean age of the patients was 54.62 ± 15.46 years. Laboratory investigations revealed mean serum calcium, phosphorus, and vitamin D levels of 9.56 ± 0.65 mg/dL, 3.53 ± 0.79 mg/dL, and 25.05 ± 12.96 ng/mL, respectively. This study demonstrated a significant correlation between serum calcium levels and the maximum diameter of urinary stones (correlation = 0.313, P-value = 0.005). No other significant associations were found between serum calcium, serum phosphorus, and serum vitamin D levels and the number of kidney stones, stone laterality, and type of kidney stone. There was also no significant difference between the two groups. Conclusions: In conclusion, the role of serum calcium, phosphorus, and 25-(OH) vitamin D levels in urinary stone formation remains controversial. This study suggests that there is no significant association between serum calcium, phosphorus, or 25-(OH) vitamin D and urinary stones, except for a positive association between serum calcium and the diameter of the stone.