Welfare of dairy cows can be assessed using welfare assessment protocols consisting of resource, management and animal-based measures. Welfare Quality® Assessment Protocol is one of the best-known protocols, which depends almost entirely on animal-based measures. To gain more objective and rapid welfare assessment, new techniques have been developed to measure welfare of animals, such as hair cortisol concentration. As cortisol is released in response to stress, it has long been used as a biomarker of stress in animals. While the precise mechanism of cortisol incorporation into hair is unknown, hair cortisol concentration seems to be a marker of long-term systemic cortisol concentration. Hair cortisol is, therefore, a potential marker of chronic stress and is not likely to be affected by acute stress. Studies on cattle show connections between hair cortisol concentration and factors such as pregnancy, parity, diseases, ectoparasites, body condition score, environmental changes, stocking density and milk yield. Hair cortisol concentration appears to be affected by time of sampling, cow age and breed, UV radiation, season, body region of sampled hair and hair colour. Its concentration also depends on sampling and analytical methods. Hair cortisol is a promising non-invasive tool to evaluate welfare of dairy cows, however, more research is needed to determine the extent of effects on its concentration and the appropriate method of sampling and analysis. Correlations between Welfare Quality® Assessment Protocol scores and pooled hair cortisol concentrations have not yet been found, and more research is needed with larger sample size, a standardized protocol of hair sampling, processing and analysis. With proper attention to detail, hair cortisol levels in pooled hair samples might come to be used as a reliable indicator of dairy animal welfare.