This research was carried out at Plant Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Egypt, during 2018/2019 ginning season. The main objective of this research is tracking cotton fiber quality and foreign matter content through the ginning and cleaning systems. Three different seed cotton levels; namely, Good to fully good (G/FG), Good (G) and Fully Good fair to Good (FGF/G) of Giza 86 long staple Egyptian cotton cultivar, in addition to three methods of cleaning; i.e., two hand cleaning methods as belt, mesh and control treatments. Lint cotton samples collected at each cleaning methods were analyzed for foreign matter content and ginning efficiency to produce fiber for High Volume Instrument (HVI) fiber analyses. Mesh system; gave the highest mean values of the ginning efficiency parameters, i.e. gin stand capacity (0.92 kg lint/inch/hr.), lint percentage (37.65 %), lint grade code (26.83) and the lowest value of the ginning time (1.62 hr./kentar). The highest mean values for spinning consistency index (176.88), upper half mean length (32.14mm), length uniformity index (86.10%), fiber bundle strength (38.28 g/tex), maturity index (0.87), micronaire reading (4.23) and fiber reflectance degree (Rd;72.66%) were registered by the same cleaning method. The seed cotton level Good to Fully Good (G/FG) surpassed the seed cotton level Fully Good Fair to Good (FGF/G) in the ginning efficiency parameters and High Volume Instrument (HVI) fiber properties. The most studied HVI fiber properties were insignificantly (p < /em> > 0.05) affected by the interaction between the methods of seed cotton cleaning and seed cotton level (A × B) except, the fiber length parameters (upper half mean length [UHML], short fiber index [SFI]) and the reflectance degree ((Rd %).