Background: Nowadays Percutaneous Nephrolithotomy (PCNL) is performed in prone and supine positions. Physiologic solutions should be used to irrigate during PCNL. Irrigation can cause hemodynamic, electrolyte and acid-base changes during PCNL. Objectives: The current study aimed to compare the electrolyte, hemodynamic and metabolic changes of prone and complete supine PCNL. Patients and Methods: It was a randomized clinical trial study on 40 ASA class I and II patients. Twenty of patients underwent prone PCNL (Group A) and the other twenty underwent complete supine PCNL (Group B). The two groups received the same premedication and induction of anesthesia. Blood pressure (systolic, diastolic and mean) and pulse rate were recorded before, during and after anesthesia and Hb, Hct, BUN, Cr, Na, and K were also measured before and after operation in the two groups. The volume of irrigation fluid, total effluent fluid (the fluid in the bucket and the gazes) and volume of absorbed fluid were measured. Results: There were no significant differences in Na, K, BUN, Cr, Hb and Hct between the two groups. Absorption volume was significantly different between the two groups (335 ± 121.28 mL in group A and 159.45 ± 73.81 mL in group B, respectively) (P = 0.0001). The mean anesthesia time was significantly different between the two groups (P = 0.012). There was a significant difference in bleeding volume between supine and prone PCNL (270.4 ± 229.14 in group A and 594.2 ± 290 in group B, respectively) (P = 0.0001). Mean systolic blood pressure during operation and recovery was 120.2 ± 10.9 and 140.7 ± 25.1 in group B, and 113.4 ± 6.4 and 126.2 ± 12.7 in group A, respectively. Systolic blood pressure between the two groups during operation and recovery was significantly different (P = 0.027 and P = 0.022, respectively). Mean diastolic blood pressure in supine group during operation and recovery was 80.53 ± 7.57 and 95.75 ± 17.48, and 73.95 ± 3.94 and 83.4 ± 12.54 in prone group, respectively. Diastolic blood pressure was significantly different between the two groups. It was 80.55 ± 7.57 and 95.75 ± 17.48, respectively during operation and recoveryin the supine group and 73.95 ± 3.94 and 83.4 ± 12.54 in the prone group, respectively (P = 0.001 and P = 0.014, respectively), but there was no significant difference between the pulse rate mean value of the two groups. Conclusions: The electrolyte and metabolic changes were not significantly different between the two groups, and although fluid absorption in prone group was more than that of the complete supine group, there was no significant difference between the two groups. Considering advantages of complete supine PCNL such as less hemodynamic changes (less hypotension, less fluid absorption and less duration of operation) this kind of PCNL was recommended.