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Invasive fungal infections are a major cause of morbidity and mortality in immunocompromised children and premature neonates. The new class of echinocandin lipopeptides offers alternative options for treatment and prevention through a distinct mechanism of action, broad spectrum antifungal activity against Candida and Aspergillus spp., linear pharmacokinetics, few relevant drug–drug interactions and excellent tolerance. Micafungin has been the first echinocandin approved in Europe for the use in children of all age groups, including preterm neonates. Its favourable safety profile and documented clinical efficacy in all paediatric age groups make it an attractive choice for treatment of candidemia and other forms of invasive candidiasis and for prophylaxis of Candida infections in haematopoietic stem cell transplant and severely neutropenic patients. This article reviews the clinical development of micafungin and provides an update on pharmacokinetics, safety and dosing of the compound in paediatric age groups.