This review article describes genetics investigations of DNA from human skeletal remains. In the molecular genetic laboratory at the Institute of Forensic Medicine, molecular genetic identifications of the World War II mass grave victims are performed. The characteristics of ancient DNA and the environmental factors which affect its preservation are described. The recommendations for excavation, storage and molecular genetic identification of skeletal remains are presented. Reference samples from relatives and samples for the elimination database are collected and analyzed for each mass grave. The most appropriate type of bones and teeth for genetic analyses are described and the measures for preventing contamination are listed. Procedures for DNA extraction, DNA quantification, DNA typing of autosomal microsatellites, Y chromosome microsatellites and mitochondrial DNA are described and statistical calculations of match probability are exposed.