Research on ancient DNA (aDNA) has the potential to enable molecular biologists and archeologists to decipher certain aspects of history by direct looking into the past. However, several major problems in this field limit the applicability of aDNA studies, most importantly contamination with modern DNA and postmortem DNA degradation. In this study we extracted and analyzed aDNA obtained from ~3500 year-old human and animal skeletal remains from two burial sites in north-western Iran. We attempted to determine the species of origin for the animal bones using general primers that allow amplification of mitochondrial DNA from almost all mammalian species. In addition, we designed the experiments in a way that allows monitoring the overall rate of potential contamination. In order to investigate the level of biomolecular preservation we employed HPLC (High Performance Liquid Chromatography) analyses to measure the extent of amino acid racemization. Despite the fact that amino acid preservation was low, we successfully extracted DNA from all samples. The data revealed that the level of contamination with human DNA was higher than the amount of DNA originating from other sources. Also, the frequency of DNA sequences from pig and horse was higher than other species. In general, while our data suggest that aDNA can provide valuable information on such ancient samples, the retrieval of aDNA is still a challenge due to both the problem of contamination with modern DNA and degradation of endogenous DNA.