Epstein-Barr Virus (EBV) DNA presents in the serum of nasopharyngeal carcinoma (NPC) patients indicates the existence of the viral DNA in the circulation and may be used as an early marker in NPC diagnosis. EBV DNA isolated from the serum and then amplified by using polymerase chain reaction (PCR) could be used to assess the response of the DNA to various NPC therapies. This study compares the results of EBV DNA measurement in the serum of NPC patients using photoelectrochemical technique and PCR. The presence of a specific oligonucleotide sequence of a standard DNA (EBNA-1) may be detected by photoelectrochemical hybridization of the standard with a DNA probe immobilized on TiO2 electrode, in which the DNA is intercalated by an electrochromic material. The purpose of this study is to obtain a photoelectrochemical system with a relatively good response and sensitivity to the changes in the concentration of EBV DNA in the peripheral blood serum of NPC patients. This research attempts to provide a device and methods that are simple, relatively inexpensive and easy to use, yet sensitive enough to see the prognosis of NPC patients. This study also attempts to develop the measurement instrumentation technology in the field of biomedical research. The photoelectrochemical system of this research used anthocyanin as DNA intercalator. The anthocyanin was isolated from purple cabbage leaves (also known as red cabbage), strawberries, and grapes and the extractant of these anthocyanins were ethanol and water. The best extraction with the highest level of total anthocyanin was achieved by alcohol as extractant. Alcohol gave higher yield of anthocyanin compared to water and ethyl acetate. Purple cabbage leaves have the highest level of anthocyanin compared to strawberry fruits and grapes. Anthocyanins contained in the extract of purple cabbage, strawberries, and grapes may function as DNA intercalators. Electrochromic substance used as DNA intercalator produces difference between the current strength generated by photoelectrochemical system with light and without light. There is a very strong correlation between diluted concentration of DNA and current strength shown by the electrochemical system of this study. There is also correlation between EBV EBNA-1 DNA concentration readings by using photoelectrochemical system and PCR. The sensitivity and specificity to EBV DNA in the serum of NPC patients of photoelectrochemical techniques are significantly higher compared to PCR.