The Crystallinity Index is a measure of structural order in bone and is potentially an extremely useful tool in bioarchaeology since it can assist in sequencing bones into chronological and/or stratigraphic order, act as an indicator for preservation, and assist in reconstructing burning events. Unfortunately, concerns over influencing variables and bone sampling issues inhibit full and wide-spread adoption of this approach. An attempt has been made to determine the influence of a number of internal and external variables on bone crystallinity changes. CI, C/P and C/C were calculated using Fourier Transform Infrared Spectroscopy - Attenuated Total Reflectance (FTIR-ATR) on modern burned and unburned faunal bone. Samples were taken systematically across bone elements and on the internal and external surfaces. The CI results support previous work and show increases with burning intensity. It is also shown that extrinsic variables (such as temperature and duration of burning) have more of a significant influence on CI values than intrinsic variables (such as location of sample site on the bone). A sampling strategy is suggested for those wishing to use the CI on bone in archaeological contexts.