The National Reference and Consultant Laboratories in Germany play a valuable role for the scientific progress in the field of medical microbiology. They cover the entire spectrum of infectious agents from prions, viruses and bacteria to parasites and contribute substantially to laboratory capacity in Germany. The continuous development of the reference laboratory structure is of key importance to ensure public health microbiology. Here, we aim to inform the scientific community of the structure of the German National Reference and Consultant Laboratories and give an update on their activities in the surveillance of pathogens in Germany.