Purpose We aimed to assess critical temperature areas in the kidney parenchyma using magnetic resonance thermometry (MRT) in an ex vivo Holmium:YAG laser lithotripsy model. Methods Thermal effects of Ho:YAG laser irradiation of 14 W and 30 W were investigated in the calyx and renal pelvis of an ex vivo kidney with different laser application times (tL) followed by a delay time (tD) of tL/tD = 5/5 s, 5/10 s, 10/5 s, 10/10 s, and 20/0 s, with irrigation rates of 10, 30, 50, 70, and 100 ml/min. Using MRT, the size of the area was determined in which the thermal dose as measured by the Cumulative Equivalent Minutes (CEM43) method exceeded a value of 120 min. Results In the calyx, CEM43 never exceeded 120 min for flow rates ≥ 70 ml/min at 14 W, and longer tL (10 s vs. 5 s) lead to exponentially lower thermal affection of tissue (3.6 vs. 21.9 mm2). Similarly at 30 W and ≥ 70 ml/min CEM43 was below 120 min. Interestingly, at irrigation rates of 10 ml/min, tL = 10 s and tD = 10 s CEM43 were observed > 120 min in an area of 84.4 mm2 and 49.1 mm2 at tD = 5 s. Here, tL = 5 s revealed relevant thermal affection of 29.1 mm2 at 10 ml/min. Conclusion We demonstrate that critical temperature dose areas in the kidney parenchyma were associated with high laser power and application times, a low irrigation rate, and anatomical volume of the targeted calyx.