Differentiating renal oncocytoma from its renal cell carcinoma (RCC) mimics, particularly chromophobe RCC, can be difficult, especially when limited tissue is available for evaluation and requires sophisticated microscopic, ultrastructural and immunohistochemical evaluation. In this review, the relevant literature has been reviewed, and supporting data obtained by applying modern microarray-based technologies are discussed with a focus on molecular pathology of renal oncocytoma. The high resolution whole-genome DNA-microarray based analyses excluded with all certainty the occurrence of small specific alterations. Renal oncocytomas are characterized by variable chromosomal patterns. The number of genes selected by global gene expression analyses and their usefulness in the diagnostic pathology based on immunohistochemical evaluation is far below the expectations. The conflicting staining patterns, together with the poor specificity of proposed antibodies, leads us to believe that these candidate immunomarkers might not help in the separation of these tumors. Applying DNA based tools might help in the diagnosis of renal oncocytoma with uncertain histology. However, only the combination of all available techniques could give reliable information.