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Introduction Microbiology culture is the "gold standard" for diagnosis of fungal infections; however, culture has a lengthy turnaround time. A more timely assessment is possible with cytology and Gomori-methamine silver (GMS) staining. Materials and methods A total of 100 respiratory tract specimens with a positive fungal Gomori-methamine silver stain and corresponding culture were selected. The cytology slides were reviewed for factors contributing to discrepant results. Specimens were classified as 2 types of variances: interpretative and sampling. Concordant diagnoses were also evaluated. Results Eighty-two cases had fungal organisms that grew in culture. The remaining 18 cases were composed solely of fungal organisms that did not grow in culture (17 cases with Pneumocystis jirovecii ; 1 case with Pityrosporum ovale ). These 18 cases were excluded from the variance analysis. Thirty-three of 82 cases (40%) had concordant cytology and microbiology results, whereas 49 cases were discrepant. Variances were both sampling (41 cases) and interpretive (8 cases). Interpretive variances were predominantly Aspergillus species misinterpreted as Candida . Difficulty identifying true septate hyphae was the major contributing factor for misinterpretation. Conclusions Cytologic evaluation of respiratory specimens remains a useful preemptive diagnostic tool in the rapid diagnosis of fungal infection. Cytology samples significantly contribute to the diagnosis of respiratory fungi. However, interpretive variances between Aspergillus and Candida organisms are common. Awareness of the characteristic features that distinguish fungal organisms can further improve the diagnostic utility of cytology.