This study was conducted to determine the effectiveness, in terms of cleaning efficiency and fiber quality, of the seed cotton cleaning stages installed in cotton gins that process predominately spindle-harvested, irrigated Upland cotton and to determine the effect of the various processing stages during ginning on gin turn out and fiber quality. The study showed that the average amount of trash content present in seed cotton was typically < 10%. The seed cotton cleaning process was able to remove 20 to 40% with the remainder of the trash removed by subsequent lint cleaning stages. The study also showed that the gin stand has no influence on fiber quality provided that the gin stand was not overloaded, maintained to manufacturers recommendations, and moisture levels maintained within the recommended levels. Flow-through air lint cleaners had no significant effect on fiber quality with minimal reduction in trash. The controlled-batt saw lint cleaners had positive and significant effects on color and trash; negative effects on length, length uniformity, short fiber and nep content, elongation; and no effect on strength, micronaire, fineness, maturity, number and size of SCN and fiber nep size. The batt-less saw lint cleaners had similar effects on fiber quality, although not as severe. The controlled-batt saw lint cleaners were more aggressive than the batt-less saw lint cleaners and removed more trash and hence achieved a better color grade, with this improvement resulting in notable reductions in lint turn out, fiber length, and increased short fiber and nep content.