Dairy cow welfare can impact both the economic performance of an individual farm and the public perception of the sector, thus influencing the sustainability of the dairy farming industry. Intensive dairy farming in Iran started in the 1940s, but there is limited data available regarding dairy cattle welfare in the country. Therefore, the aim of this study was to design and use a comprehensive bespoke welfare assessment protocol in intensive Iranian dairy farms to provide baseline data for Iran and other countries with similar farming systems. The protocol consists of animal-based, stockperson-based, and resource-based measures. The first part of the welfare assessment protocol (being presented in this paper) was developed from the existing literature and contained 11 animal-based and 2 stockmanship measures. The protocol was applied in 62 intensive dairy cattle farms in five arid and semi-arid provinces of Iran. Welfare Quality sample size suggestions were used to reach the minimum sample size for all animal-based measures except for the locomotion score, where either the whole milking herd was scored or all cows in the early lactation (<
150 days in milk) group. Results show that there was a good focus on nutrition management on the farms. Lameness prevalence and the incidence of hock lesions were too high, although within the range seen in many housed cows outside Iran. In addition, 13.5% of cows had damaged ears. The prevalence of dirty legs was high (≥80% of cows), and the hygiene score was unrelated to the farming system. Finally, the extremely high median prevalence of tail damage (60%) indicates a significant welfare issue that needs to be addressed with urgency.