Chicken cystatin variant I108T is a mutant in the hydrophobic core of the molecule. It has shown many amyloid-prone characteristics in our previous experimental study. To explore the detailed structural and dynamic properties of the amyloidogenic mutant I108T, 10 ns molecular dynamic simulations of the I108T mutant and wild-type chicken cystatins were performed in this study. Our results suggested that the I108T mutant, which exhibited larger secondary structural fluctuations and hydrophobic core expanding tendency compared with the wild-type chicken cystatin, is a new amyloidogenic form of chicken cystatin, and therefore supported the hypothesis to some extent that site mutations in the hydrophobic core might induce the domain swapping.