The performance of delinted cotton seeds and of naturally infected samples, considering both localization and amount of inoculum has not been studied extensively so far. This work was carried out with the objective of evaluating the effect of Colletotrichum gossypii South. on naturally infected and artificially inoculated seeds. Seeds were inoculated by keeping them in direct contact with the developing colony of the fungous in agar medium (PDA) during different exposure periods. Part of both treated and non-treated seed samples was dissected into fractions - teguments and embryos. Both fractions and a number of whole seeds of the same samples were analysed separately. The following parameters were evaluated: C. gossypii incidence through incubation in modified filter paper (addition of agar 0,5% to the substrate); seed germination in paper roll, and disease index of seedlings on the 7th day of age. In the main, the inoculum of C. gossypii was internal in seeds. Seed desinfestation increased the germination percentage up to 54% and decreased the index disease to around 45%.