Purpose <p>The recommendation for urinary stone metaphylaxis is based on urinary stone analysis. It is not known to what extent the separate analysis of the core and shell differ and can therefore possibly influence the metaphylaxis.</p> Methods <p>Included were 19,973 stone analyses from 2021 to 2022 using infrared spectroscopy. For mixed stones, the individual components were specified semi-quantitatively in 5% increments. While 62% of the stones were analyzed using a representative sample of the whole stone, a separate core-shell analysis was performed in 38%. Analysis focused on evaluating the distribution of the most common urinary stone minerals.</p> Results <p>In 22.9% of cases, difference in analysis between core and shell could be measured, in 13.6%, analyses differed by at least 10%. Here, a clear shift in the distribution of stone types compared to the distribution using a single representative probe could be demonstrated: Calcium oxalate occurred significantly less frequently in this group (50.2% vs. 73.3%), while struvite (5.9% vs. 2.7%) and carbonate apatite (25,2% vs. 12.1%) occurred significantly more frequently. The number of components detected in the stones increased in separate analysis and were even more when core and shell differ. In 4.3%, the main component between core and shell changed.</p> Discussion <p>In 13.6% of stones, there were clinically significant differences between core and shell. The change in the main component between core and shell may indicate the stone genesis. Separate core-shell analysis can influence and possibly optimize the metaphylaxis. Especially in the high-risk situation and recurrent stones, a separate core-shell analysis may be beneficial.</p>