Sepsis is a significant public health concern worldwide, with high morbidity and mortality. With regard to a targeted antimicrobial treatment strategy, the earliest possible pathogen detection is of crucial importance. Until now, culture-based detection methods represent the diagnostic gold standard, although they are characterized by numerous limitations. Culture-independent molecular diagnostic procedures may represent a promising alternative. In particular, droplet digital PCR (ddPCR) is a novel one-step PCR assay that achieves higher accuracy and sensitivity in detecting causing pathogens in patients with bloodstream infections.