BackgroundCervical cancer is causally related to cervical infections by oncogenic human papillomavirus (HPV) genotypes. To improve the quality of diagnosis evaluation of screening methods and their HPV type detection rate is an important part for this item. ObjectivesTwo different cervical specimens of the same patients were analysed simultaneously with molecular HPV subtyping methods to find the most sensitive sample material for cervical cancer screening. Study designBiopsy specimens and cytological smears of the cervix of 443 patients were analysed for human papilloma virus (HPV) subtyping by a macroarray from Chipron, Germany, which allows a differentiation of 16 high and 16 low risk types. Results were compared for reliability and differences were studied. ResultsBoth sample material groups showed HPV conformity of 70%, 23% more subtypes could be detected in smears in contrary to biopsies but only 6% vice versa. 14 biopsies and 7 smears were HPV negative although the concerning second sample type of the patients was HPV positive. HPV 16 as one of the most relevant subtypes in cervical cancer pathogenesis was missed in the biopsies’ group with 34.3% out of 35 HPV 16 positive smear cases, whereas only one smear failed to discover this subtype contrariwise. ConclusionComparison of the examination results shows that subtyping of smear samples is able to detect more subtypes than by biopsy specimens. The probability to underdiagnose HPV 16 and to get a false negative result in bioptic sample material favours smear as method of choice for HPV subtyping.