The purpose of this paper is to analyse productivity change of Estonian dairy farms during the period 2001-2009. Data envelopment analysis (DEA) was used to estimate the technical efficiency of producers and Malmquist productivity index for analysis of productivity change. Estonian FADN data was used in analysis. Performed analysis indicated that Estonian EU accession in 2004 increased considerably total factor productivity. Farm gate milk prices have considerable effect on total factor productivity change. Number of cows and milk yield has positive and dependence on subsidies, stocking density and capital to working hours ratio have negative effects on total factor productivity change.