Petvious research on performance of farmer association (FA) in Taiwan mostly aimed at the credit department of FA. Few study has studied the operational efficiency of FA as a whole. In this paper, we attempt to build up aggregate multi-dimension input output indexes of FA for assessing performance of FAs. The three-stage DEA model developed by Fried et, al (2002) was revised to consider the possible effect from environmental variables. Results showed that in 2000 the average technical efficiency of FAs in Taiwan was 0.788, which implied a 21.2% capacity for further improvement. Ignorance of effects of environmental variables on efficiency measurement would result in an underestimation efficiency level by about 22.7%. Results also indicated that average efficiency of urban type FAs was greater than that of mixed and rural type FAs. FAs in region is not statistically signification different. In addition, a FA with high percentage of young staff and low branches number tended to perform better.