Clinical metagenomics (CMg) refers to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information. Due to the increasing access to next-generation sequencing (NGS) facilities, CMg is a gast-growing field. In this context, we held the second International Conference on Clinical Metagenomics (ICCMg2) in Geneva in October 2017. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. Besides, we also discuss the evolution of CMg from the last conference held in 2016. In brief, many technical issues related to CMg are expected to be successfully addressed in the coming years. Conversely, assessing the clinical value of CMg, implementing a quality process, storage of data and the ethics of CMg are emerging challenges.