Using recent advances in the stochastic production frontier framework, this paper presents an empirical analysis of technical, allocative and economic efficiency of a sample of organic and conventional cotton farms located in Greece. The results suggest that both farm types in the sample examined are technically, allocatively and economically inefficient. Farmer's age and education and farm size are important factors in explaining differentials in efficiency estimates. In comparative terms, organic farms exhibit lower efficiency scores vis-à-vis their conventional counterparts in terms of technical and economic efficiency; regarding allocative efficiency both farm types are almost equally inefficient. Low efficiency scores in both types of farming may be attributed to the respective intervention policies of the last 20 years.