Currently, indications for flexible ureterorenoscopy (fURS) are expanding, mainly due to technological advancements. Although data from clinical series definitely presents fURS as a safe procedure, serious complications including sepsis and ureteral lesions do occur. These complications seem to be a result of the unique elements of fURS, ureteral access and irrigation, pushing normal upper urinary tract physiology into pathophysiological processes, including intrarenal/pyelo-veneous backflow and ureteral contractions, potentially resulting in septic, haemorrhagic and ureteral lesional complications. Knowledge on normal upper urinary tract physiology are crucial for understanding how these harmful effects of fURS may be avoided or minimized. The pathophysiology of intrarenal pressure increases and ureteral access will be discussed as a basis for understanding preventive measures. Role of antibiotics, ureteral access sheaths, safty guidewires, pain medication, prestenting and pharmacologic modulation of pyeloureteral dynamics are reviewed from a pathophysiological perspective.