Free electron laser has been developed as tunable lasers over a wide range of wavelengths. Devices irradiating in the region of 6–16μm (1666–625cm −1 ) are operable in the Beijing free electron lasers facilities (BFEL). For understanding the interactions between FEL and biological tissues, in this study wavelength-selective infrared-induced structure changes of substances under irradiation by FEL were measured using FT-IR spectroscopy. The carboxyl acids and carboxylates samples investigated include salicylic acid, sulfosalicylic acid, cholic acid, deoxycholic acid, sodium cholate and sodium deoxycholate. The changes of the FT-IR spectra of the molecules prove that the spectral variations of the samples induced by FEL are closely related to their hydrogen bond networks.