Introduction: Epidemiology of fungal infections in an infectious disease reference centre is different from other institutions. This study aimed to look at the scenario of fungal infections at an infectious disease reference centre in Malaysia. Methods: All positive fungal cultures from an infectious disease reference centre were identified by routine mycology laboratory methods. Patient demographic, laboratory and clinical data were collected and analyzed. Duplicate data were excluded. Results: Middle-aged Malay males were the most common group. However, increased proportions of Chinese, Myanmar and Indonesians reduced the Malay predominance in HIV-positive group. In all patients, Candida species represented 64.1% isolates, followed by Cryptococcus neoformans (14.7%) and Penicillium marneffei (14.7%). Among HIVpositive individuals, C. neoformans (37.9%) was the most common species, followed by P. marneffei (35.6%) and all Candida species (17.2%). In contrast to other non-infectious disease reference centres, common causes of fungaemia included P. marneffei (43.5%), Candida species (25.8%), C. neoformans (24.2%) and H. capsulatum (6.5%). Conclusion: The prevalence of fungal infection at an infectious disease reference centre is different from other non-infectious disease reference centres. This may have an impact on current antifungal practice especially empiric antifungal therapy, patient morbidity and mortality.