The vulnerability of children has long raised ethical concerns resulting in the lack of inclusion of children in research studies. This has impeded the development of relevant medical therapies specific for children. In response to these circumstances, international policies have begun to recognize the need to carry out research focused on children. Translational HIV infection research is highly dependent on many factors including the availability, quality, and traceability of samples and their associated data under a strict system of quality management. The primary objective of the Pediatric HIV BioBank is to contribute to the furthering of scientific knowledge about vertical HIV infection. To achieve this aim, the BioBank processes, stores, and provides distinct samples from HIV/AIDS children to research projects free of charge. Strict compliance to ethical norms is always guaranteed. At present the Pediatric HIV BioBank has 429 vials containing different sample types from 243 vertically HIV-infected children. The Pediatric HIV BioBank represents a novel approach to HIV research that might be of general interest not only for basic and clinical research teams working with HIV, but also for those groups trying to establish large networks focused on researching specific clinical problems. It also represents a model to stimulate cooperative research on specific clinical problems. The main objective of this article is to show the structure and function of the Pediatric HIV BioBank that allow it to efficiently provide samples to different research projects in Spain and in other countries.