The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on diagnostic microbiology was held in Lausanne from 25 ^th to 28 ^th September 2018. A total of 87 participants from 31 countries participated to this postgraduate technical workshop. Over 4 days, the mornings were dedicated to talks, which covered many subjects including MALDI-TOF, molecular diagnosis, genomics and metagenomics as well as new innovative approaches. The afternoons were dedicated to 12 different practicals covering various aspects of microbiological diagnosis. This ESCMID meeting provided a unique opportunity to exchange knowledge and ideas on the recent tools developed in diagnostic laboratories. This meeting report summarises the key messages of this four-day workshop.