Focal segmental glomerulosclerosis (FSGS) is a progressive kidney disease, and mitochondrial disease known to be a primary malady for secondary FSGS. Mitochondrial nephropathy with FSGS is diagnosed by genetic analysis or electron microscopy when it is suspected. As adequate morphologic features to diagnose mitochondrial nephropathy by light microscopy are lacking, this study used 10 cases with genetically proven mitochondrial disease and analyzed the kidney samples obtained by biopsy (n = 7) or autopsy (n = 3). We found granular swollen epithelial cells (GSECs) among the distal tubuli and collecting ducts in all patients, whereas such features were absent in IgA nephropathy, primary FSGS, and interstitial nephritis. Ultrastructural analysis of GSECs displayed accumulation of abnormal-shaped mitochondria in GSECs. To test whether GSECs were really associated with mitochondrial mutations, laser-captured single GSECs in 1 case with a position where 3,271 mutation were measured using a single-cell PCR analysis. This revealed that the mutant load of GSECs was significantly higher than normal-appearing epithelial cells within the same sample (63.4 + or - 17.8% vs. 32.5 + or - 4.6%; P <0.0001). This is direct evidence that GSEC is a characteristic cellular feature, indicating cells with mutant mitochondrial DNA accumulation. In addition, the incidence of GSECs did not correlate with serum creatinine levels, proteinuria, percent glomerulosclerosis, tubulointerstitial changes, or arteriolar hyalinosis, suggesting that GSECs per se may not cause tissue damage. In conclusion, GSEC is a distinct morphologic feature suggesting mitochondrial nephropathy and is a useful tool to identify secondary FSGS on the basis of mitochondrial abnormalities.