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Efficient DNA extraction procedures, as well as accurate DNA amplification, are critical steps involved in the process of successful DNA analysis of skeletal samples. Unfortunately, at present there is no infallible method to recover DNA from highly degraded samples due to variations in DNA yield from larger bone fragments, which may be attributed to heterogeneity within bones. We evaluated two different protocols for bone decalcification in the DNA extraction procedure for bones. This study is important for analysis of challenging forensic samples.