Background <p>Nephrocalcinosis, characterized by excessive calcium deposition within the renal parenchyma, can be a long-term complication of anorexia nervosa (AN). The extent of renal calcification can range from molecular-level alterations to macroscopic stone formation, contributing to progressive kidney injury. While early detection is critical for prognosis, limited studies have characterized the structural and elemental composition of renal calcifications associated with AN. Here, we report a case of nephrocalcinosis in the setting of AN.</p> Case presentation <p>A 25-year-old woman with AN presented with progressive renal dysfunction and gouty arthritis. Renal biopsy revealed focal tubulointerstitial nephritis with extensive calcification. Conventional light microscopy identified crystalline deposits within the tubular lumen, but further characterization required advanced imaging techniques. Low-vacuum scanning electron microscopy (LV-SEM) of formalin-fixed paraffin-embedded (FFPE) specimens demonstrated more widespread crystalline deposits than were visible by routine histopathology. Elemental analysis via energy-dispersive X-ray spectrometry (EDX) confirmed that the deposits were primarily composed of calcium phosphate.</p> Conclusions <p>These findings underscore the utility of LV-SEM/EDX in detecting and characterizing renal calcifications at high resolution. The ability to perform elemental analysis on FFPE tissue sections provides a novel and practical approach for elucidating the pathogenesis of nephrocalcinosis. These methods may enhance the accuracy of renal crystal identification, thereby facilitating earlier diagnosis and improved management of nephrocalcinosis.</p>