Purpose: The management of early- (EOS) and late-onset sepsis (LOS) and neonatal intensive care units (NICUs) has not been extensively evaluated. Methods: 231 highly specialized level 1 and level 2 NICUs in Germany were asked to participate in an internet-based survey. Results: The final analysis of anonymized datasets from 80 NICUs (response rate 34.6 %) compared university hospitals and regional neonatal referral centers. The survey describes potential areas of improvement concerning empirical treatment of infants with LOS with vancomycin and 3rd generation cephalosporins, minimal volume of blood sampling for aerobic culture, consideration of lumbar tap in any child with blood culture positive LOS and drug monitoring details for gentamicin and vancomycin. Conclusion: In summary, this survey reveals a significant gap between recent national German guidelines and daily practices in German NICUs.