Miniaturization of ureteroscopy materials is intended to decrease tissue damage. However, tissue hypoxia and the gross and microscopic effects on tissue have not been adequately assessed. We compared the gross and microscopic effects of micro-ureteroscopy (m-URS) and conventional ureteroscopy (URS) on the urinary tract. We employed 14 pigs of the Large White race. URS was performed in one of the ureters with an 8/9.8 F ureteroscope, while a 4.85 F m-URS sheath was used in the contralateral ureter. Gross assessment of ureteral wall damage and ureteral orifice damage was performed. For microscopic assessment hematoxylin-eosin staining and immunohistochemistry for detection of tissue hypoxia were conducted. Regarding the macroscopic assessment of ureteral damage, substantial and significant differences were recorded using URS (C = 0.8), but not with m-URS. Microscopic assessment after staining with hematoxylin-eosin revealed greater epithelial desquamation in the URS group (p < 0.05). Pimonidazole staining revealed greater hypoxia in the epithelial cells than in the remainder of the ureteral layers. We conclude that m-URS causes less damage to the ureteral orifice than URS. Histopathological findings show m-URS reduces ureteral epithelial damage compared with conventional ureteroscopy. Both URS and m-URS cause cellular hypoxia.