Human plasminogen undergoes a large tertiary structural change in the presence of lysine derivatives (e.g. ε-amino caproic acid, EACA). This change facilitates human plasminogen activation by human plasminogen activators, resulting in elevated blood plasmin levels. It is hypothesized that this structure-function relationship is similar for bovine plasminogen. The objectives of this study were to investigate the effect of the ligand EACA on the secondary structure of plasminogen (bovine, human, and rabbit) and the tertiary structure of bovine plasminogen using Fourier-transform infrared spectroscopy (FTIR). Spectra of plasminogen, EACA, and a mixture of plasminogen and EACA in water and deuterium were collected using FTIR. Fourier-self deconvoluted spectra in the amide I region (1700–1600 cm−1) were used to detect changes in secondary structure of plasminogen after EACA addition. Change in bovine plasminogen tertiary structure was determined by comparing ratios of amide II (1600–1500 cm−1) to amide I bond intensities over time for samples in deuterium. No differences in secondary structure were observed for any plasminogen in the presence of EACA; however, addition of EACA significantly changed tertiary structure of bovine plasminogen. This tertiary structural change indicates a transition from a folded to an unfolded state, which could be more easily converted to plasmin. These results are consistent with reported human plasminogen studies using neutron scattering (tertiary structure) and circular dichroism (secondary structure) methods.