We present a novel polarization alignment technique based on windowed Fourier-transform (WFT) spectral interferometry to determine the wavelength-dependent orientation of the principal polarization axes of photonic crystal fibers (PCFs). To test the technique, a commercially available, 82.5-cm-long HC-800-02 type hollow-core PCF was measured. The angles belonging to the fast and the slow principal axes of the fiber were determined from the peak intensity values of the ridges in the WFT map at different wavelengths. We demonstrate that the orientation of the principal polarization axes of the tested PCF is wavelength-dependent. The precision of the angle measurement was better than 0.3°.