Properly controlling the cotton ginning process increases fiber yields and monetary returns to the cotton farmer, improves fiber length distribution, and reduces short fibers, neps and seed-coat fragments. A computerized process control system that utilizes the cotton market price and the performance characteristics of gin machinery to determine the optimum machinery sequence is now available. Cotton moisture, color, and foreign matter measurements are made with electronic devices at three stations in the gin system and are used to control the gin process. Special routing valves are used to bypass or select any combination of seed cotton cleaners, dryers, and lint cleaners. When gin machinery is bypassed, the quantity of marketable lint is increased and the amount of fiber damage is decreased.