The aim of our study was to compare the nephrotoxic effects of liposomal Amphotericin B (Ambisome) and Amphotericin B lipid complex (Abelcet) on rat kidneys at short (14 days) and long term (28 days) treatment applications. Thirty-six male Wistar rats were included and divided into six groups (n=6). Groups 1 and 4 are composed as control groups by administrating intraperitoneal (ip) 0, 9 molar Serum physiologic for a period of 14 and 28 days respectively. Group 2 and 3 are treated with 5 mg/kg Ambisome and 5 mg/kg Abelcet for 14 days respectively, Group 5 and 6 are treated with same agents for 28 days respectively. Then, the rats were transcardially perfused, samples were taken from cortex and medulla regions of kidneys. The micrographs of group 1 and 4 were seen as normal. For short term treatment, some morphological changes were seen in proximal tubule cells in group 3 whereas in group 2 the graphs were observed as normal. However, after long term drug using in group 5 and 6 there were vacuolization, increased lysosomal structures and deep basal folding's into tubular cells lumen. These experiments establish that renal damage were seen in short and long term use of Abelcet and long term use of Ambisome.