The impact of climate change on cotton yields in seven main arable crop sites in Greece (Agrinio, Alexandroupolis, Arta, Karditsa, Mikra, Pyrgos, Yliki) was investigated. The FAO AquaCrop (v.4) water driven model was used as a crop development simulation tool under eight climatic models (HadRM3, C4I, REMO MPI, ETHZ, CNRM, DMI-HIRHAM, KNMI, SMHI) based on IPPC’s A1B Climate Change scenario. The mean values of the models ensemble for temperature and precipitation were +1,8˚C until 2050 and +4 ˚C until the end of the century. The respective values for precipitation were -11% and -24%. The research was applied over three periods, 1961-1990, 2021-2050 and 2071-2099. AquaCrop validation for yield, biomass and canopy cover in respect to field data obtained from experiments carried out in Karditsa (Central Greece) from 2005 to 2007 was satisfactory on the account of Root Mean Square Error (0.17 to 0.49) and Index of Agreement (0.93 to 0.94). AquaCrop model was run using the Growing Degree Day mode in order to account better for the temperature variations. However, it gave erratic results for some specific climatic models (SMHI, KNMI, CNRM) in some years within the period 1961-1990. The predicted yields were highest in locations of western Greece (Agrinio, Arta, Pyrgos), whereas north-eastern Greece (Alexandroupolis) appeared to be less favoured by climate change. A tendency towards increasing yields by the end of the century was detected for the majority of the models. The efficiency of the eight models for yield predictions in the seven sites was assessed by means of a discriminant function analysis. On the account of their function coefficients over the seven sites, it was found that the models DMI and C4I explained consistently a great proportion of variation among the three time periods whereas the models ETHZ, SMHI and KNMI were more efficient in the periods 1961-1990, 2021-2050 and 2071-2099 respectively