Defect of apple was depreciated the product value and causes storage disease seriously. To detect the defect of ‘Fuji’apple with machine vision system, the optical characteristics of defect should be investigated. In this research, absorbance spectra of defect were acquired by spectrophotometer in the range of visible and NIR region(400∼1,100nm) and L*a*b* color values were also acquired by colorimeter. NIR machine vision system was constructed with B&W camera, frame grabber, 16 tungsten-halogen lamps, variable focal length lens and NIR bandpass filter which was mounted to lens outward. Average gray values of defect at 15 NIR wavelength were acquired and the significant NIR wavelength was selected by comparing Mahalanobis distance between sound and defective apple. As the result of Mahalanobis distance analysis, the significant wavelength to discriminate the defectives in ‘Fuji’apple were found to be 720nm for scab and 970nm for bruise and cuts and 920nm was also effective regardless of defective types.