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Cotton blue disease (CBD) is the viral disease which poses the greatest threat to cotton in Brazil. One efficient way of controlling this disease is by using resistant cultivars. However, the recent emergence of an atypical form of CBD (ACBD), caused by a new virus genotype capable of overcoming these resistant cultivars, is causing concern. Thus, the aims of this study were to evaluate the distribution of ACBD in the states of Mato Grosso (MT) and Goias (GO), to determine the relationship between vector infestation level, disease incidence and yield, and to check the reaction of cotton cultivars to two viral isolates. In both cotton production areas, 1128 plots were surveyed and 6.5% showed plants with the virus, 97.3% and 2.7% with ACBD and CBD, respectively. In cultivars susceptible to ACBD, a positive linear relationship between changes in the levels of aphid infestation and incidence of viral infection was indentified, and a negative linear relationship between infestation level and yield. The maximum acceptable level of aphids up to 80 days after sowing for susceptible cultivars was approximately 15%. Although 83% of the cultivars were shown to be resistant to CBD, only 19.2% were resistant to ACBD. There was also a number of cultivars with considerable resistance to both isolates.