An encoder output signal correction apparatus for correcting two-phase sinusoidal signals with a phase difference output from an encoder, comprising: a third harmonic calculator calculating at least one of an amplitude (a 1, a 3) and a phase (φ 3) of third harmonic component contained in said two-phase sinusoidal signals on the basis of a variation in radius of a Lissajous waveform of amplitude-, phase-, and offset-corrected two-phase sinusoidal signals, and a corrector correcting a third harmonic distortion in said two-phase sinusoidal signals on the basis of at least one of a amplitude (a 1, a 3) and a phase (φ 3) calculated by said third harmonic calculator, wherein said third harmonic calculator derives a frequency signal component through a Fourier analysis of a variation in radius of said Lissajous waveform by calculating a real part (Re) and an imaginary part (Im) of a Fourier transform using following recurrence equation: Re = Re + dRe Im = Im + dIm, wherein dRe = ∑ i = 0 N − 1 r i cos 2 π 4 N i dIm = ∑ i = 0 N − 1 r i sin 2 π 4 N i, wherein said third harmonic calculator divides one turn of said Lissajous waveform into N uniform sector zones, and derives a representative value r i of radiuses of each of said sector zones i corresponding to Θ1 (i=0 to N-1), the representative value r i of a radius of each of said sector zones i being calculated using an averaging method in which radiuses r m at a plurality of points in the sector zone i are derived in order to obtain the representative value r i by equation: r i = 1 M ∑ m − 1 M r m, wherein the amplitude a 1 is obtained by a 1 = 1 N ∑ i = 0 N − 1 r i, and wherein r i is the representative value of a radius of a sector zone i, and N is the number of sector zones i into which one turn of said Lissajous waveform is divided, and the amplitude a 3 and the phase φ 3 are obtained by a 3 = 1 2 N 2 Re 2 + Im 2, φ 3 = tan − 1 Im Re. a third harmonic calculator calculating at least one of an amplitude (a 1, a 3) and a phase (φ 3) of third harmonic component contained in said two-phase sinusoidal signals on the basis of a variation in radius of a Lissajous waveform of amplitude-, phase-, and offset-corrected two-phase sinusoidal signals, and a corrector correcting a third harmonic distortion in said two-phase sinusoidal signals on the basis of at least one of a amplitude (a 1, a 3) and a phase (φ 3) calculated by said third harmonic calculator, wherein said third harmonic calculator derives a frequency signal component through a Fourier analysis of a variation in radius of said Lissajous waveform by calculating a real part (Re) and an imaginary part (Im) of a Fourier transform using following recurrence equation: Re = Re + dRe Im = Im + dIm, wherein dRe = ∑ i = 0 N − 1 r i cos 2 π 4 N i dIm = ∑ i = 0 N − 1 r i sin 2 π 4 N i, wherein said third harmonic calculator divides one turn of said Lissajous waveform into N uniform sector zones, and derives a representative value r i of radiuses of each of said sector zones i corresponding to Θ1 (i=0 to N-1), the representative value r i of a radius of each of said sector zones i being calculated using an averaging method in which radiuses r m at a plurality of points in the sector zone i are derived in order to obtain the representative value r i by equation: r i = 1 M ∑ m − 1 M r m, wherein the amplitude a 1 is obtained by a 1 = 1 N ∑ i = 0 N − 1 r i, and wherein r i is the representative value of a radius of a sector zone i, and N is the number of sector zones i into which one turn of said Lissajous waveform is divided, and the amplitude a 3 and the phase φ 3 are obtained by a 3 = 1 2 N 2 Re 2 + Im 2, φ 3 = tan − 1 Im Re.