Pathogens such as Toxoplasma gondii, lentiviruses (e.g., CAE), Hypoderma spp., Neospora caninum, Mycoplasma spp., and pestiviruses are important for goat farming in Lithuania; however, data on their prevalence remain limited. To address this gap, a multi-pathogen study was conducted between 2021 and 2024 using selected ELISA kits (ID.vet, Innovative Diagnostics, France). A total of 380 blood samples were collected from 30 goat herds across different regions of Lithuania; the sample size varied depending on the pathogen. Serum samples were tested for antibodies, and seroprevalence was calculated for each pathogen. The highest seroprevalence was detected for T. gondii (38.9%, 143/368) and CAE virus (19.5%, 74/380). Antibodies to Mycoplasma spp. (0.3%, 1/368), Hypoderma spp. (3.8%, 7/184), and N. caninum (0.5%, 2/368) were detected only sporadically, while no antibodies to Border disease virus or Q fever were identified. Mixed infections were found in 7.6% of samples. Chi-square analysis showed that co-infections with toxoplasmosis and CAE occurred more frequently than expected (χ² = 19.05, p < 0.001). Herd size was significantly associated only with CAE seroprevalence (χ² = 7.913, df = 1, p < 0.05). Overall, toxoplasmosis and CAE were identified as the most epidemiologically relevant infections in the Lithuanian goat population.