Headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) have traditionally been used, in combination with other analyses, for the chemical characterization of organic residues recovered from archaeological specimens. Recently in many life science fields, comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS) has provided numerous benefits over GC-MS. This study represents the first use of HS-SPME-GC×GC-TOFMS to characterize specimens from an experimental modern reference collection. Solvent extractions and direct analyses were performed on materials such as ivory, bone, antlers, animal tissue, human tissue, sediment, and resin. Thicker film column sets were preferred due to reduced column overloading. The samples analyzed by HS-SPME directly on a specimen appeared to give unique signatures and generally produced a higher response than for the solvent-extracted residues. A non-destructive screening approach of specimens may, therefore, be possible. Resin and beeswax mixtures prepared by heating for different lengths of time appeared to provide distinctly different volatile signatures, suggesting that GC×GC-TOFMS may be capable of differentiating alterations to resin in future studies. Further development of GC×GC-TOFMS methods for archaeological applications will provide a valuable tool to uncover significant information on prehistoric technological changes and cultural behavior.