Invasive fungal infections of immunocompromised patients cause major problems in modern medicine and only a limited number of effective antifungals are available, making the identification of new drug targets a priority. The inhibition of primary metabolism represents a promising therapeutic strategy, but a better understanding of the metabolic processes during pathogenesis is required. Infection, invasion and maintenance within a host are very dynamic events and fungal metabolism has to adapt to these changes. Glycolysis, gluconeogenesis and starvation all contribute to successful host colonisation, but the temporal and spatial resolution of their specific importance is poorly understood. Knowledge about the metabolic requirements of pathogenic fungi during infection could lead to the identification of new classes of antifungals, which allow the treatment of otherwise life-threatening infections.