Introduction: The etiological agents of onychomycosis are dermatophyte fungi, nondermatophyte filamentous fungi (NDFF), and yeasts. Nail clippings are an accurate tool for diagnosing onychomycosis. The objective of this study was to correlate the characteristics of fungi observed in nail clipping examinations with the results for agents isolated in culture, indicating whether the fungus found on microscopy is a dermatophyte, NDFF, or yeast. Methods: An observational descriptive study of onychomycosis nail clippings stained with PAS comparing culture results with microscopic criteria of fungi morphology, arrangement/orientation, and location of organisms in the nail and presence of neutrophils, serous lakes, and bacterial colonies was conducted. Results: Thirty-three nail clippings from 29 participants were analyzed. A statistically significant correlation (p < 0.05) was found between smooth/thin/long hyphae with a “combed” pattern and dermatophyte agents (sensitivity 89.4%, specificity 91.5%), and between irregular/thick/short anarchic distributed hyphae and nondermatophytes (sensitivity 61.5%, specificity 89.4%). No statistical association with region where fungi were in the nail or with the presence of neutrophils, serous lakes or bacteria was found. Small, rounded, yeast-like organisms correlated with Candida infection. Conclusions: Although not a substitute for culture, microscopic analysis of fungal structures offers good accuracy for differentiating agents of onychomycosis.