Introduction: Kidney diseases affect millions of people worldwide. Over several decades, electron microscopy has been an integral part of the kidney biopsy study repertoire. Objectives: In this study, we assessed the role of electron microscopy in the diagnosis of kidney diseases. Patients and Methods: This was a retrospective cross-sectional study conducted at a referral center over a 16-year period (2001-2016). The electron microscopy (EM), light microscopy (LM), and immunofluorescence (IF) profiles of the patients were assessed. The final diagnosis was based on EM, and the primary LM results were compared to those of EM in order to assess the contribution rate of EM to the final diagnosis. The role of EM was categorized as essential, helpful, or non-contributory. Results: A total of 2006 kidney biopsies were performed. Male subjects accounted for 44.3%, and adults for 74.1% of the cases. The most common diagnosis was lupus nephritis (LN) (20.7%), followed by focal segmental glomerulosclerosis (FSGS) (15.7%) and membranous glomerulonephritis (MGN) (14.5%). EM was the most contributory in hereditary nephritis and minimal change disease (MCD). Overall, EM was essential in 25.2%, helpful in 17.4%, and non-contributory in 57.4% of all 2006 cases. Conclusion: The common kidney disorders in this geographic area of Iran are LN, FSGS, and MGN. In about half of the patients, EM study played an important role in the more accurate diagnosis of kidney diseases and prevented misdiagnosis. This role has been found to be more prominent in inherited diseases. We recommend EM as a useful and indispensable tool for routine pathologic study of biopsies when possible.