PCV-3 and PCV-4 are novel viruses that can infect domestic pigs and wild boars. Both viruses are associated with multiple disorders in domestic pigs (reproductive failure, respiratory damage, etc.). However, the clinical impact on wild boars remains unknown. This study aimed to assess the presence of these viruses in wild boars from mid-western Spain and their sanitary impact on the species. A total of 166 submandibular lymph nodes were collected from hunted wild boars, along with available information about their reproductive status, lung injuries, body condition, and tuberculosis status. The samples were used to detect PCV-3 and PCV-4 using real-time PCR. In total, 84.9% of the sampled animals were positive for PCV-3, and 33.7% were positive for PCV-4. The detection of PCV-4 was more frequent in wild boars that had received supplementary feeding, suggesting that the direct contact favored by this practice could increase the transmission of this virus in wild boar populations. The infections did not seem to influence the body condition, reproductive status, lung lesions, or TB lesion severity patterns in the studied animals. Thus, although these viruses have been widely detected throughout wild boar populations from the studied area, they do not seem to be a health threat to this species. Nevertheless, their monitoring in wild boars is recommended, as they are often in contact with extensively reared pigs, which are susceptible to these viruses.