Squamous cell carcinoma (SCC) represents the most common malignant tumour of the eye and external genitals in horses. Comparable to humans, papillomaviruses (PV) have been proposed as etiological agents of cancer in horses and recently, Equine papillomavirus type 2 (EcPV2) has been identified in genital SCCs. Hitherto it had never been demonstrated in ocular SCCs. The first goal of this study was to determine the prevalence of EcPV2 DNA in tissue samples from equine genital and ocular SCCs, genital papillomas and penile intraepithelial neoplasia (PIN) lesions, using EcPV2-specific PCR. The second goal was to investigate the possibility of latent EcPV2 infection in the genital and ocular mucosa of healthy horses on swabs obtained from the eye, penis, vulvovaginal region and cervix. EcPV2 DNA was detected in all genital SCCs (17/17), genital papillomas (8/8), PIN lesions (11/11) and ocular SCCs (9/9). In healthy horses, EcPV2 DNA was detected in 43% (17/40) of penile swabs, 53% (9/17) of vulvovaginal swabs, 47% (8/17) of cervical swabs and 57% (32/56) of ocular swabs. This study confirms the presence of EcPV2 DNA in equine genital SCCs. Moreover, we demonstrate for the first time its involvement in other genital lesions and in ocular SCCs and latent EcPV2 infections in normal genital (including cervical) and ocular equine mucosa. The close relatives of EcPV2 are associated to cutaneous lesions, and this virus is not related to high-risk human papillomaviruses causing cervical cancer. Thus, similar viral tropism does not imply close evolutionary relationship.