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Background: Our purpose was to study the relationship of the 3 different types of endoscopic calcifications of the renal papilla (Randall's plaque, intratubular calcification, papillary crater) with the type of stone and urine analysis. Methods: This prospective study examined 41 patients (age range: 18 to 80 years) who received retrograde intrarenal surgery (RIRS) for renal lithiasis (mean stone size: 15.3 ± 7.2 mm). The renal papilla injuries were endoscopically classified as Randall's plaque, intratubular calcification, or papillary crater. Calculi were classified as uric acid, calcium oxalate monohydrate (COM; papillary and cavity), calcium oxalate dihydrate (COD), or calcium phosphate (CP). A 24 h urine analysis of calcium, oxalate, citrate, phosphate, and pH was performed in all patients. The relationship of each type of papillary injury with type of stone and urine chemistry was determined. Fisher's exact test and Student's t-test were used to determine the significance of relationships, and a p value below 0.05 was considered significant. Results: The most common injury was tubular calcification (78%), followed by Randall's plaque (58%), and papillary crater (39%). There was no significant relationship of Randall's plaque with type of stone. However, endoscopic intratubular calcification (p = 0.025) and papillary crater (p = 0.041) were more common in patients with COD and CP stones. There were also significant relationships of papillary crater with hypercalciuria (p = 0.036) and hyperoxaluria (p = 0.024), and of Randall's plaque with hypocitraturia (p = 0.005). Conclusions: There are certain specific relationships between the different types of papillary calcifications that were endoscopically detected with stone chemistry and urine analysis. COD and CP stones were associated with endoscopic tubular calcifications and papillary craters. Hypercalciuria was associated with tubular calcification, and hypocitraturia was associated with Randall's plaque.