Drug amiodarone (AMIO) is vital for the anti-arrhythmic patient, but it has numerous adverse effects. The lacrimal gland is accessory apparatus essential for tear production, which is critical for visual functions, so this study aims to investigate the effect of AMIO on it. Three groups' rabbits from both sexes (2-2.5 kg), each group containing five rabbits, were used in this study. The experiment was carried out in the following manner: one of these groups functioned as a control and got an intraperitoneal injection of normal saline. The second group received an intraperitoneal injection of AMIO (80 mg/kg BW) once daily for two weeks. The third group received a daily dosage of AMIO (160 mg/kg BW) intraperitoneally for two weeks. The obtained FTIR spectra revealed that the molecular structure of the lacrimal gland is sensitive to AMIO treatment. The AMIO treatment caused considerable changes in the frequencies and bandwidths of the NH-OH region's functional groups. The stretched C-H region, used as an indicator of lipid status, also changed significantly, particularly at the higher AMIO dosage (160 mg/kg). Significant alterations in α-helix and β-turn contents were observed in the amide I of the AMIO higher dosage treated group. In conclusion, the short-term administration period of AMIO is associated with conformational and structural changes in the lacrimal gland's molecular structure, especially lipids and proteins structure.