Neps and seed coat fragments are impurities in ginned fibers causing severe problems in textile processing during spinning and dyeing. This study was designed to investigate genotypic variation of neps and seed coat fragments remaining in ginned fibers in an introgressed population. Two hundred lines of a population, i.e., JohnCotton (JC) germplasm, derived from multiple crosses between Gossypium hirsutum L. and G. barbadense L. and five cultivars were planted at two locations in 2006 and one location in 2007 with two replicates each. Neps and seed coat fragments were measured using Advanced Fiber Information System. Genotypic variations of nep count and seed coat nep (SCN) count in the JC germplasm were highly significant (P<0.001). Wide ranges of nep count (70 to 288 cnt g-1) and SCN count (2.7 to 16 cnt g-1) were identified among the 200 lines. The mean of the SCN in JC population was not significantly (P<0.05) different from the mean of the cultivars. Lint yield was negatively (favorably) correlated with nep count (r=-0.47) and SCN (r=-0.31). Unfavorable correlations were identified for nep count vs. fineness (r=-0.75) and SCN count vs. fiber bundle strength (r=0.60). Nep count was unfavorably correlated to 2.5% span length (r=0.56), but not correlated to 50% span length (r=0.10). Two lines were selected with nep count less than 90 cnt g-1 and fineness lower than 180 mg km-1 and nine lines were selected with SCN less than 6 cnt g-1 and strength greater than 230 kN m kg-1.