Treponema denticola is an oral spirochete associated with the periodontal diseases. A great deal of the molecular components of T. denticola will be learned soon since its genome sequence project is on the way. One of the most important works after genome sequence is to analyze the function of these genes and their regulation. However, like many other oral pathogens, there are currently a very limited number of molecular and genetic tools available to study gene expression in T. denticola. In this article, we describe a method of adapting differential display polymerase chain reaction (ddPCR) for use in the T. denticola system. To test for effectiveness of this protocol, we used three different temperature conditions, 4 degrees C, 25 degrees C and 42 degrees C, to test for differential gene expression. With various ddPCR conditions, we found a number of genes that were expressed differentially. Some of these differentially expressed genes were cloned and sequenced and found to be homologous with the known temperature-regulated genes, including HtrA. The study indicates that the ddPCR method can be effectively used in T. denticola for analyzing gene expression under various conditions.