Ancient DNA (aDNA) research involves invasive and destructive sampling 
procedures that are often incompatible with anthropological, anatomical, and 
bioarcheological analyses requiring intact skeletal remains. The osseous 
labyrinth inside the petrous bone has been shown to yield higher amounts of 
endogenous DNA than any other skeletal element; however, accessing this 
labyrinth in cases of a complete or reconstructed skull involves causing major 
structural damage to the cranial vault or base. Here, we describe a novel 
cranial base drilling method (CBDM) for accessing the osseous labyrinth from the 
cranial base that prevents damaging the surrounding cranial features, making it 
highly complementary to morphological analyses. We assessed this method by 
comparing the aDNA results from one petrous bone processed using our novel 
method to its pair, which was processed using established protocols for sampling 
disarticulated petrous bones. We show a decrease in endogenous DNA and molecular 
copy numbers when the drilling method is used; however, we also show that this 
method produces more endogenous DNA and higher copy numbers than any postcranial 
bone. Our results demonstrate that this minimally-invasive method reduces the 
loss of genetic data associated with the use of other skeletal elements and 
enables the combined craniometric and genetic study of individuals with 
archeological, cultural, and evolutionary value.