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The multiplex analysis system described here allows simultaneous typing of one short tandem repeat (STR) and three single nucleotide polymorphisms (SNPs) that are associated with obesity and/or osteoporosis. Genes that are related to a high body mass index (BMI) and/or a high bone mineral density (BMD) are presumed to give an advantage in surviving famines. This analysis system makes it possible to genotype the (TTTA)n polymorphism of CYP19 and three SNPs, namely the rs1800795 polymorphism of IL6, the rs373 6228 polymorphism of LRP5 and the rs993 9609 polymorphism of FTO, in a single PCR amplification in recent and ancient DNA samples. Furthermore, it allows a synchronous authentication of the results with the (TATC)n polymorphism of D13S317, the (TCTA)n polymorphism of D21S11 and the (TTTC)n polymorphism of FGA in a partial genetic fingerprinting. For this purpose, PCR products for fragment-length analysis, as well as those for sequence analysis, were amplified together. After amplification, the PCR product was split into two aliquots. The first aliquot was used for fragment-length analysis and the second one for sequence analysis. The analysis system described here has been optimized for analysing ancient samples, since only minimal amounts of material are available.