This study aimed to describe a distinct subpopulation of azoospermic patients with isolated elevation of follicle-stimulating hormone (iFSH) and poor outcomes of microdissection testicular sperm extraction (microTESE). Methods: A retrospective analysis of microTESE outcomes was conducted among 565 patients with non-obstructive azoospermia (NOA). Testicular pathology was assessed by the dominant histological pattern and Bergmann-Kliesch score (BKS). Descriptive statistics were presented for the iFSH subgroup. Inhibin B levels, the sperm retrieval rate (SRR), and BKS were compared in iFSH patients and other NOA patients. Results: The overall SRR was 33.3% per microTESE attempt. The median BKS was 0.6 (interquartile range, 0–2). Of all NOA patients, 132 had iFSH, and microTESE was successful only in 11 of those cases, with an SRR of 8.3%, while the total SRR in other NOA patients was 38.1% (p<0.001). iFSH had a sensitivity of 32.1% (95% confidence interval [CI], 27.4%–36.8%) and specificity of 94.1% (95% CI, 90.8–97.5%) as a predictor of negative microTESE outcomes. Conclusion: Patients with iFSH may harbor a distinct testicular phenotype with total loss of the germ cell population and poor outcomes of surgical sperm retrieval.