Introduction Next Generation Sequencing (NGS) platforms have radically changed the field of genomics and are routinely applied to a variety of functional genomics problems. Although NGS has markedly accelerated multiple areas of genomics research it is a massively parallel process and generates unprecedented volumes of data which present challenges and opportunities for data management, storage, and, most importantly, analysis and interpretation. The Molecular Biodiversity Laboratory (MoBiLab), located in Bari at the CNR-IBBE, is a NGS research infrastructure, realized within the LifeWatch European infrastructure for Biodiversity. In MoBiLab, skills and advanced facilities for molecular and bioinformatics analyses are integrated to provide the scientific community with services and counselling for molecular biodiversity studies. MoBiLab has started the set up of a quality management system based on Good Laboratory Practices (GLPs) accompanied by a Laboratory Information Management System (L.I.M.S.) in order to assure the highest levels of reliability, reproducibility and traceability of the results. Methods GLPs are considered a quality system aimed at ensuring safety, reliability and reproducibility of the non-clinical tests on chemicals intended for the use on human, animal and environment. GLPs are mandatory in OECD countries for preclinical tests, but may be also considered as a reference for laboratory management systems outside their main scope, that can be referred to as “GLP-like” quality systems. The L.I.M.S. is a computer system capable of handling the Acquisition stages-Processing-Storage of all data generated by a laboratory and/or processes, minimizing the risk of errors and increasing the information security. Results The internal quality system of MoBiLab has been designed by taking into account the progressive evolution of Good Research Practices. The team has first outlined a description of the main process by means of a Supplier-Input-Process-Output-Customer-like flowchart which includes the person in charge for the activity and the related documented information (Standard Operation Procedures, SOP, and records). After having identified the SOPs, researchers were provided with a template and with the instructions to draft them. In parallel, management procedures were defined by the whole team, drafted, and supported by flowcharts and other quality tools. MoBiLab, in collaboration with the Italian company Eusoft, started to develop and optimize a L.I.M.S. platform for managing all the laboratory activities through a suite of integrated modules. The platform is structured starting from the SIPOC-like flowchart and the modules are developed and customized in agreement to the SOPs. A CAPA (Corrective Action/Preventive Action) system is also going to be implemented within the LIMS. Conclusions and Perspectives The implementation of some Lean tools in the production process of the MoBiLab will be the next task of the project.