Pomegranate production in India is 772000 MT in 2011-2012 (NHB Database 2012), which is considered as very nutritive fruit, rich in vitamin B, vitamin A, thiamine, riboflavin, niacin, vitamin C and minerals (potassium, calcium, magnesium, phosphorus, iron). For consumer awareness and export quality grade, grading and sorting of fruits is necessary. Defect of internal break down causes browning or blackening of arils, which gives a typical foul smell if unnoticed. These internal defects cannot be identified from external appearance, which is a serious threat to the pomegranate processing industry as well as export resulting in rejections and quality reduction. X-ray inspection has a distinct advantage over other detection techniques, as it is non-destructive imaging of interior features of sample which detects internal defects. Soft X-ray emission spectroscopy is an experimental technique for determining the electronic structure of materials. A continuous soft X-ray system with a semi-conductor detector was used to detect the internal quality of the fruit. Thus the present study is one of soft X-ray technique to find the internal defects in pomegranate. As to conquer and sustain the international market, there is a need for export of high quality products with no internal defects. The objectives of this study is to determine the internal defects in pomegranate using soft x ray and to develop the algorithm for classification of defective pomegranate from healthy one.