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Invasive fungal infections (IFIs) are life threatening, with high morbidity and mortality. Diagnosis is challenging in our environment where there is paucity of data. The majority of laboratories in the region employ only conventional diagnostic tests. This report documents the frequency and therapeutic outcomes of invasive fungal infections diagnosed at the Lagos University Hospital over a fourteen month period. From May 2012 to July 2013, all cases from consults sent to the clinical microbiologists for review and patients with positive samples were identified from the mycology laboratory registers. Hospital based frequency of Invasive Fungal Infections was 42.5%. Patients' ages ranged from 5 days to 71 years with a median of 29 years ±20.6 SD. There were 2 cases of cryptococcal meningitis, 7 cases of candidaemia, 1 case of mucormycosis, 3 cases of invasive aspergillosis and 4 cases of fungal keratitis. Causative organisms were Candida albicans, non Candida albicans, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Fusarium scolani, Scedosporium apiospermiun, and Cryptococcus neoformans. There was an IFI case fatality rate of 47.06%. Serious fungal infections exist in our environment; however they are under diagnosed due to lack of diagnostic acumen; this impacts negatively on the management of the groups of patients at risk for these infections.Keywords: Invasive fungal infections; mucormycosis; candidaemias; keratitis; aspergillosis; cryptococcal meningitis; Lagos, Nigeria.