Nephrolithiasis is one of the most common urological conditions with a huge socio-economic impact. About 50% of recurrent stone-formers have just one lifetime recurrence and >10% of patients present with a high recurrent disease requiring subsequent and sometimes multiple surgical interventions. The advent of new technology has made endourological procedures the pinnacle of stone treatment, including procedures like percutaneous nephrolithotomy (PCNL), retrograde intrarenal surgery and miniaturized PCNL procedures. Researchers have primarily focused on comparisons with respect to stone-free rates, procedure parameters and post-operative complications. However, the effect of these three procedures on renal function or indexes of renal injury has not been sufficiently examined. This was only reported in a few studies as a secondary objective with the use of common and not the appropriate and detailed renal parameters. This review presents current literature regarding the use of novel and highly predictive biomarkers for diagnosing acute kidney injury, discusses potential mechanisms through which endourological procedures for renal stone treatment may affect renal function and proposes areas with open questions where future research efforts in the field should focus.