Contamination has vital role in deciding the quality of cotton apart from essential properties such as length, strength, fineness. Contamination of raw cotton can take place at every step i.e. from the farm picking to the ginning stage. Contamination, even if it is a single foreign fiber, can lead to the downgrading of yarn, fabric or garments or even the total rejection of an entire batch and can cause irreparable harm to the relationship between growers, ginners, merchants, spinner and textile and clothing mills. An International Textile Manufacturers Federation (ITMF) reported that claims due to contamination amounted to between 1.4 – 3.2% of total sales of 100% cotton and cotton blended yarns. A fairly large number of cotton fibers recognition researches are based on RGB color space. So in this project a system is implemented to find contaminant of cotton so that it can be used with surety. Contaminant or Foreign fibers are detected from cotton on bases of layer separation and thresholding.