Human papillomavirus (HPV) 52 and 58 are oncogenic HPV types prevalent in Asia. Our study aims to explore intratypic variants of HPV 52 and 58 in Taiwan. A total of 11,923 women were enrolled from seven townships in 1991–1992. HPV DNA in their cervical cells was detected and typed by EasyChip® HPV blot. Among 424 participants infected with HPV 52 and/or 58, nucleotide variations were determined in cervical cell samples of 406 participants by the polymerase chain reaction sequencing of the long control region, E6 and E7 genes. Nonprototype‐like variants including lineages B and C were detected in 278 (99.3%) of 280 HPV 52 samples. The prototype and prototype‐like group (lineage A) of HPV58 was found in 132 (98.5%) of 134 HPV 58 samples, with sublineage A1, A2 and A3 variant in 14.2, 27.6 and 56.7%, respectively. Among women infected with single HPV 52 type, the C variant (vs. B variant) was associated with an increased prevalence of cytologically diagnosed high‐grade squamous intraepithelial lesion or worse lesions showing an age‐adjusted odds ratio (95% confidence interval, CI) of 5.2 (1.0–27.6) and an increased prevalence of histologically confirmed high‐grade cervical intraepithelial neoplasia or more severe lesions with an age‐adjusted odds ratio (95% CI) of 7.6 (1.3–43.8). It was concluded that frequency distributions of HPV 52 and 58 variants in Taiwan were different from those in European and American populations. The association between C variant of HPV 52 and prevalence of cervical neoplasia needs further validation.