AbstractThis Scientific Opinion addresses a European Commission's mandate on the welfare of dairy cows as part of the Farm to Fork strategy. It includes three assessments carried out based on literature reviews and complemented by expert opinion. Assessment 1 describes the most prevalent housing systems for dairy cows in Europe: tie‐stalls, cubicle housing, open‐bedded systems and systems with access to an outdoor area. Per each system, the scientific opinion describes the distribution in the EU and assesses the main strengths, weaknesses and hazards potentially reducing the welfare of dairy cows. Assessment 2 addresses five welfare consequences as requested in the mandate: locomotory disorders (including lameness), mastitis, restriction of movement and resting problems, inability to perform comfort behaviour and metabolic disorders. Per each welfare consequence, a set of animal‐based measures is suggested, a detailed analysis of the prevalence in different housing systems is provided, and subsequently, a comparison of the housing systems is given. Common and specific system‐related hazards as well as management‐related hazards and respective preventive measures are investigated. Assessment 3 includes an analysis of farm characteristics (e.g. milk yield, herd size) that could be used to classify the level of on‐farm welfare. From the available scientific literature, it was not possible to derive relevant associations between available farm data and cow welfare. Therefore, an approach based on expert knowledge elicitation (EKE) was developed. The EKE resulted in the identification of five farm characteristics (more than one cow per cubicle at maximum stocking density, limited space for cows, inappropriate cubicle size, high on‐farm mortality and farms with less than 2 months access to pasture). If one or more of these farm characteristics are present, it is recommended to conduct an assessment of cow welfare on the farm in question using animal‐based measures for specified welfare consequences.