The objective of the present study was to determine the composition of various layers of upper urinary stones and assess the mechanisms of stone nucleation and aggregation. A total of 40 integrated urinary tract stones with a diameter of >0.8 cm were removed from the patients. All of the stones were cut in half perpendicularly to the longitudinal axis. Samples were selected from nuclear, internal and external layers of each stone. Fourier transform infrared spectroscopy (FT‑IR) was adopted for qualitative and quantitative analysis of all of the fragments and compositional differences among nuclear, internal and external layers of various types of stone were subsequently investigated. A total of 25 cases of calcium oxalate (CaOx) stones and 10 cases of calcium phosphate (CaP) stones were identified to be mixed stones, while 5 uric acid (UA) calculi were pure stones (purity, >95%). In addition, the contents of CaOx and carbapatite (CA.AP) crystals in various layers of the mixed stones were found to be variable. In CaOx stones, the content of CA.AP in nuclear layers was significantly higher than that of the outer layers (32.0 vs. 6.8%; P<0.05), while the content of CaOx was lower in the inner than in the outer layers (57.6 vs. 86.6%; P<0.05). In CaP stones, the content of CA.AP in the nuclear layers was higher than that in the outer layers (74.0 vs. 47.3%; P<0.05), while the content of CaOx was lower in the inner than in the outer layers (7.0 vs. 40.0%; P<0.05). The UA stones showed no significant differences in their composition among different layers. In conclusion, FT‑IR analysis of various layers of human upper urinary tract stones revealed that CaOx and CaP stones showed differences in composition between their core and surface, while all of the UA calculi were pure stones. The composition showed a marked variation among different layers of the stones, indicating that metabolism has an important role in different phases of the evolution of stones. The present study provided novel insight into the pathogenesis of urinary tract stones and may contribute to their prevention and treatment.

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