A modified non-radioactive single strand conformation polymorphism analysis incorporating a temperature gradient (TG-SSCP) and temperature gradient gel electrophoresis (TGGE) were evaluated for the detection of human papillomavirus type 6 (HPV 6)-variants in 41 condylomata acuminata and 5 Buschke-Loewenstein tumours. TG-SSCP and TGGE analysed part of the transforming ORF E6 of HPV 6 spanning nucleotides 10 to 495. TG-SSCP distinguished between 8 HPV 6-variants whereas TGGE demonstrated 6 different DNA-species. HPV 6-strains found in Buschke-Loewenstein tumours did not vary in the analysed portion of the E6 ORF as compared to ordinary condylomata acuminata. TG-SSCP and TGGE further showed absence of double infection with different HPV 6-strains in the analysed samples. Our results demonstrated that both methods may be successfully used for the detection of different strains of microbiological agents, although TG-SSCP seemed to provide easier execution and to confer a higher degree of flexibility than TGGE.