Fourier-transform near infrared spectroscopy (FT-NIR) has been used in assessment of sectioned or pulverised teeth, and some consideration has been given to intact teeth in context of demineralisation and decay. This study considered the use of FT-NIR for characterization of sound (undecayed) intact teeth, both inside and outside custody bags. Replicate spectra of the same unbagged tooth were consistently grouped in principal component (PC) space, while spectra from different teeth were separated in PC space. The window of the custody bag carried a spectral signature that impacted the tooth-in-bag spectra, but subtraction of the window spectrum from tooth-in-bag spectra was successful in removal of this influence, with the corrected tooth-in-bag spectra aligning to the spectra of the same tooth outside the bag in PC space. Spectra of teeth of the same individual were discriminated from those of other individuals. Potential applications of this technology are discussed.