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Terahertz absorption spectra of poly(3-hydroxyalkanoates) with different conformations were measured by using a terahertz time domain spectrometer. Sharp absorption peaks were observed in the spectrum of crystalline samples. The orientation direction of the transition dipole moment was investigated by the polarization spectra. The peak at 2.92 THz was assigned to a vibration of helical structure along the fiber axis, and the peak at 2.49 THz was attributed to a vibration due to the hydrogen bonding between helix structures. The temperature dependence of the spectra reflects the change in the hydrogen bonding distance and melting process of the crystalline structure.