Objectives This study aimed to investigate type-specific concurrent anogenital human papillomavirus (HPV) detection and examine associations with concurrent detection. Methods Data from a Dutch repeated cross-sectional study among young sexual health clinic visitors (Papillomavirus Surveillance among STI clinic Youngsters in the Netherlands) between 2009 and 2019 were used. Cohen’s kappa was used to assess the degree of type-specific concordance of HPV detection between anal and genital sites for 25 HPV genotypes for women and men who have sex with men (MSM) separately. Associations with type-specific concurrent HPV were identified. Receptive anal intercourse (RAI) was forced into the model to investigate its influence. Results Among women (n=1492), type-specific concurrent anogenital detection was common; kappa was above 0.4 for 20 genotypes. Among MSM (n=614), kappa was <0.4 for all genotypes. The only significant association with type-specific concurrent anogenital detection among women was genital chlamydia (adjusted OR 1.5, 95% CI 1.1 to 2.2). RAI was not associated. Conclusions Type-specific concurrent anogenital HPV detection was common among young women, and uncommon among MSM. For women, concurrent HPV detection was associated with genital chlamydia. Our results are suggestive of autoinoculation of HPV among women.