Nep and seed coat fragment (SCF) contamination in lint are potential problems for spinning and dyeing operations in textile plants. Cotton cultivars grown in three test groups of the Mississippi RCVT were processed through a typical sequence of gin machinery, ant the lint was analyzed manually for SCF and motes. The AFIS was also used to analyze neps and seed coat neps (SCN) in lint. These results were used to characterize cultivars, identify interactions between cultivar and test group, and identify trends between measurements. The most significant differences between cultivars were found for the number of AFIS neps, ranging from 660 to 720 neps/g lint. Differences were also found between cultivars in each test for the number of SCF and AFIS SCN, and differences were seen between cultivars in two tests for the number of motes. Depending on cultivar, the number of manually counted SCF ranged from 6 to 35 and averaged 13.1 SCF/g lint. The SCN counted by the AFIS ranged from 6 to 22 and averaged 11.5 SCN/g lint. The correlation coefficient between manual SCF and AFIS SCN was as high as 0.84 in one test but only 0.59 in another, so these measurements were similar but different. Only one measurement, AFIS nep count, revealed a significant interaction between cultivar and test group. For other measurements, cultivar differences were consistent between test groups.