The main objective of this project was to track cotton fiber quality and foreign matter content through the harvesting and conveying/cleaning systems on a brush-roll stripper harvester. Seed cotton samples were collected from four locations on a cotton stripper harvester in 2011 and 2012 along with handpicked seed cotton samples. The four machine locations included: 1) after the harvested cotton was conveyed out of the row unit but before being engaged by the cross auger conveyor, 2) from the separation duct inlet after the cotton was conveyed by the cross auger, 3) from the basket by-passing the field cleaner (before field cleaner, BFC), and 4) from the basket after the cotton was processed through the field cleaner. Seed cotton samples collected at each location were analyzed for foreign matter content and ginned to produce fiber for High Volume Instrument (HVI) and Advanced Fiber Information System (AFIS) fiber analyses. Results show little difference between the initial entry in the machine until the BFC location, and provide evidence that the field cleaner was the most effective system on a cotton stripper for removing foreign matter. AFIS and HVI results indicate that the harvesting, conveying, and cleaning systems had minimal effects on fiber characteristics not associated with foreign matter. Generally most parameters were not affected significantly until the seed cotton passed through the field cleaner, after which the parameters were reduced to similar levels of hand-harvested seed cotton.