Our objective was to compare human papillomavirus (HPV) detection in paired self-collected vaginal samples transported by overnight mail in liquid specimen transport medium (STM) (wet) or in dry tubes (dry). Women aged 18-24 years were recruited online to self-collect vaginal swab samples at home for HPV testing and 159 women returned paired wet and dry samples. Dry samples were rehydrated with STM upon arrival at the laboratory. HPV was detected by the Roche Linear Array HPV genotyping test (37 genotypes) and Kappa and McNemar statistics were used to compare wet versus dry samples for detecting HPV. Of the subjects tested in this study, 51 % were HPV-positive (in either sample) and 40 % were positive for high-risk HPV. A total of 216 type-specific infections were detected among the 80 HPV-positive women. Almost perfect agreement was observed between paired samples for detecting any HPV (subject-level positive agreement: 91.9 %, κ: 0.85) or type-specific HPV (positive agreement across types: 90.1 %, κ: 0.90). Similar agreement between sample types was seen when testing for high-risk types and 81.9 % of all type-specific infections were detected in both samples. Among discordant pairs, wet samples were 3.3 times more likely to be positive for type-specific HPV than dry samples (P = 0.02). However, in 63.6 % of wet-positive/dry-negative discordant pairs analysed for viral load, type-specific HPV was either undetectable or detected at a low level (<100 copies) in the wet samples, suggesting that the majority of infections missed by using dry samples are less likely to be clinically relevant. Our results indicate that dry transport is a feasible option for transporting at-home self-collected vaginal samples for HPV DNA testing.