It has been known that pitch frequency variation influences the formant frequency. In conventional studies, the data during a few pitches are regarded as stationary signals. If the estimated spectrum is the average spectrum in a few pitches, this cannot take into account the transition of formant frequencies and the influence of variation of pitch frequencies upon the vocal transfer function in each pitch period. The electroglottographic (EGG) is employed with speech data in order to cut the corresponding waveform of the glottal closure in each pitch cycle. The vocal tract transfer function of the Japanese back-low vowel /a/, front-high /i/ and back-high /u/ was estimated for Japanese adults using the Fejer kernel mapping for short time analysis estimates fundamental frequencies and glottal closure quotients also. The facts that the variation of formant frequency is related to that of pitch, and that variation has an individual difference are discussed.