BACKGROUND: Human papilloma virus (HPV) including more than 80 subtypes has been known to be associated with the utero-cervical cancer by many investigators. So, the advanced methods for detection of HPV DNA subtypes is very important for early diagnosis of clinical staging. We evaluated the efficiency between them, which were 1) hybrid capture system (HCS) and 2) multiplex polymerase chain reaction (PCR) as routine clinical laboratory tests. METHODS: HCS results including middle and high risk subtypes (HPV 16/18/31/33/35/45/51/52/56), and PCR results including beta-globin and consensus (HPV E1 gene) primers were compared on 53 pap smear samples. And multiplex PCR including HPV 16, 18 type-specific primers was done on 33 samples which revealed positive results for both HCS and consensus primers PCR. RESULTS: There was 90.5% concordance between the HCS results and consensus primers PCR results. Among the 33 samples showing positive results for both HCS and E1 consensus primers PCR. 5 samples were HPV 16, and 4 samples were HPV 18 (1 sample revealed coexistence of HPV 16 and 18) by type specific multiplex PCR. Almost all of them were class IV-V by Pap classification. CONCLUSIONS: There was high concordance between the HCS and consensus PCR for detection of HPV DNA. We concluded, with additional type-specific PCR primers, the multiplex PCR was effective and beneficial method as a routine clinical laboratory diagnostic test.