A relatively straightforward high performance liquid chromatography (HPLC) method for determination of DNA methylation in flue-cured tobacco leaves was developed and validated. DNA methylation was measured as follows: DNAwas hydrolyzed to nucleotide units in perchloric acid. The bases of cytosine and 5-methylcytosine were separated on a reversed-phase C18 column at 30 degrees . The mobile phase used methanol: 5 mmol/L pentane sulfonate (10:90, v/v) and a flow rate of 0.7 mL/min. The absorbance of bases was measured at 273 nm. The results showed that the method was accurate, quick, and cost effective to determine DNA methylation of flue-cured tobacco.