This paper aims to analyze taxation on sugar and ethanol. Based on the payment of each tax, the potential tax burden on these products in all links of their chains in São Paulo state for the years 2000 and 2008 has been estimated. The results pointed to a potential tax burden of 23.04% of the final price of hydrous ethanol and 27.39% of the final price of crystal sugar in 2008. With the aim of measuring the importance of the exemption of some taxes on foreign sales, the article also estimates the difference in potential tax burden between ethanol exported and the one sold in the domestic market. The same is done for sugar. The difference of the tax burden on ethanol exported by the plant and ethanol sold to the domestic market is estimated at 15.65 pp. For sugar, this difference is 21.25 pp. Finally, in order to verify the evolution of the tax burden on the sugarcane industry, this paper estimates the tax burden on this sector for 2000, which was 40.08% for ethanol and 25.91% for sugar. There is an increasing burden on the sugar and a reduced burden on ethanol.