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Establishing the diagnosis of invasive mold infections (IMI) in immunocompromised children is challenging due to nonspecific clinical presentations and the limited sensitivity of traditional culture-based methods. Rapid non-culture-based diagnostics such as the 1,3-beta-D-glucan and galactomannan assays have emerged as promising adjuncts to conventional diagnostic tests in adults. Available data suggest that 1,3-beta-D-glucan has limited accuracy in the pediatric population and is not recommended to be used for the diagnosis of IMI in children. On the other hand, the diagnostic performance of the serum and bronchoalveolar lavage galactomannan in immunocompromised children is comparable to results observed in adults and can be used as a screening tool in children at high risk of developing invasive aspergillosis (IA) who are not receiving mold-active antifungal prophylaxis and as a diagnostic tool in symptomatic children suspected of having IA. Herein, we summarize the available evidence for the use of these rapid non-culture-based diagnostics in immunocompromised children. We also summarize potential causes of false positivity for the 1,3-beta-D-glucan and galactomannan assays.