The aim of this research was to assess welfare indicators in different dairy cow management systems, determine the prevalence of parasitic infections, and examine the impact of these infections on welfare indicators. This study was conducted in 2024 on 45 Holstein-Friesian cows aged 2 to 6 years (first to third lactation) in Northern Serbia. Monitoring was carried out in tie stall, loose, and pasture-based systems, covering three production phases: late dry period, clinical puerperium, and peak lactation. Cow welfare was evaluated using the Welfare Quality® protocol, and parasitological diagnostics from fecal samples. Identified welfare issues included a low body condition score (BCS), dirtiness of udders, flanks, and legs, integument alterations, nasal and ocular discharge, lameness, and diarrhea. Cows in the pasture-based system had significantly higher scores for dirtiness (p < 0.001), while those in tie stalls showed more integument alterations (p < 0.001). Loose-housed cows had higher nasal discharge scores (p < 0.001). Parasites identified included Eimeria spp., Buxtonella sulcata, gastrointestinal strongylids, Moniezia spp., Dicrocoelium dendriticum, Fasciola hepatica, and Paramphistomum spp. Significant correlations (p < 0.001) were found between certain welfare indicators and parasite infections, such as a low BCS with Eimeria oocysts and nasal discharge and hairless patches with Buxtonella sulcata and Dicrocoelium dendriticum. These data indicate needs for improving dairy cows’ welfare and the implementation of effective parasite control measures in all housing systems.
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