Markets for organically produced high quality cotton (Gossypium hirsutum L.) are projected to increase. Field experiments were conducted to compare the effects of two cropping systems on seed and lint yield and fiber quality of three cotton cultivars. The experiments, conducted during 2008, 2009, and 2010, were laid out in a split plot design with four replicates, two main plots (organic and conventional system) and three subplots (cotton cultivars: Athena, Alexander, and Fandom). The organic system resulted to a seed cotton yield at greater or same levels than the conventional system. Micronaire values and maturity for all the cultivars at 2009 and 2010 were satisfactory, while fiber length did not differ between cropping systems, except in 2009. Elongation of the fiber differed among cropping systems only in 2010 and Fandom had the highest rate of fiber elongation. For the organic and conventional systems, fiber strength reached values of 34.47 and 32.5 g tex -1 , respectively. Short fiber index declined throughout the 3-yr period in the organic system. This study confirmed that organic cultivation does not negatively affect lint yield or fiber quality, while in the same time it also produced high seed yield. Findings suggest that despite the significant role of genotype, the interactions of year with cultivar and cropping system have a decisive impact on fiber quality.