During a Disaster Victims Identification (DVI) mission, international protocols rely on interdisciplinary work, especially between specialists from forensic imaging and anthropology. In case of air crashes or explosions, DVI units may face thousands of fragmented human remains (FHRs). The physical re-association of FHRs and the identification process is very complex and challenging, and relies upon expensive and destructive DNA analysis. A virtual re-association (VRA) of these fragments, using Multidetector Computed Tomography (MDCT), could be a helpful tool in forensic anthropology analysis, as it could assist in reducing the number of DNA samples. However, there is no standardized protocol for including such an approach into a DVI procedure. The aim of this study was to summarize and analyze existing techniques through a systematic review and to develop a protocol for virtual re-association of FHRs, adapted to the DVI context. A keyword-based literature search was conducted, focusing on the VRA methods using MDCT imaging and 3D surface scan methodology. Reviews and primary articles, published between 2005 and 2020 in the fields of forensic anthropology, paleoanthropology, archeology, and fracture reduction surgery were sorted out. A total of 45 publications were selected and analyzed based on their content and relevance. The results show that research on the re-association of FHRs increased significantly during the last five years. Seven steps regarding the MDCT-based method for the virtual re-association of FHRs could be identified: acquisition of 3D-images, segmentation of the MDCT-data, post-processing and surface generation, identification of intact and fracture surfaces, identification and registration of matching fragments, and validation of the re-association. The literature is surprisingly sparse regarding the FHRs re-association as a forensic tool, and mainly consists in case reports, whereas validated methods were presented in archeology and surgery publications. However, we were able to adapt the MDCT-based approach for the virtual re-association of the FHRs and propose an innovative protocol for DVI missions. This protocol includes the needed details, from the acquisition of MDCT imaging to the virtual re-association of 3D models and its validation. Each step has to be fully tested, adapted and validated in future studies.