Purpose Fuchs flecks (FFs) have been previously identified at the leading edge of pterygia and may represent collections of epithelial stem-like cells that give rise to this condition. This study aims to evaluate the clinical significance of FFs in patients with ocular surface disorders, such as pterygium and pinguecula, by in vivo confocal microscopy (IVCM). Methods This study is a Single-center, retrospective, observational case series of 40 eyes from 20 patients with clinical diagnoses of pinguecula or pterygium, or both. IVCM (Rostock Cornea Module; Heidelberg Engineering, Heidelberg, Germany) was performed on patients with pinguecula or pterygium, or both. The presence of FFs on the ocular surface of patients with pterygium and pinguecula was assessed by IVCM and subsequently documented. Results FFs were present in 24 of 30 eyes (80.0%) in paired macroscopically normal nasal or limbal regions, 19 of 20 (95.0%) in pinguecula, 13 of 15 (86.7%) in primary pterygia, and 7 of 7 (100%) in recurrent pterygia. Conclusions High rates of FFs were identified at the head of pinguecula, primary pterygium, recurrent pterygium, and macroscopically normal nasal and temporal limbus. We postulate that FFs may represent precursor lesions to UV-associated ocular surface pathology. Identification of Fuchs fleck by IVCM may permit clinicians to predict the patients who may progress to develop more advanced pathology.