Plumage damage represents one of the animal-based measures of laying hens welfare. Damage occurs predominantly due to age, environment and damaging pecking. IR thermography, due to its non-invasiveness, objectivity and repeatability is a promising alternative to feather damage scoring systems such as the system included in the Welfare Quality® assessment protocol for poultry. The aim of this study was to apply IR thermography for the assessment of feather damage in laying hens kept in two housing systems and to compare the results with feather scoring. At the start of the experiment, 16-week-old laying hens (n=30) were divided into two treatments such as deep litter pen and enriched cage. During 4 months, feather damage was assessed regularly in 2-week intervals. One more single assessment was done nine and a half months after the start of the experiment. The feather damage on four body regions was assessed by scoring and IR thermography: head and neck, back and rump, belly, and underneck and breast. Two variables obtained by IR thermography were used: the difference between the body surface temperature and ambient temperature (ΔTB) and the proportion of featherless areas, which were defined as areas with a temperature >33.5°C. Data were analyzed using a GLM model. The effects of housing, time, region and their interactions on feather damage, measured by the feather scoring and by both IR thermography measures, were all significant (P<0.001). The ΔTB in all assessed regions correlated positively with the feather score. Feather scoring revealed higher damage in enriched cages compared with deep litter pens starting from week 6 of the experiment on the belly and back and rump regions, whereas ΔTB from week 6 in the belly and from week 8 on the back and rump region. The proportion of featherless areas in the belly region differed significantly between the housings from week 8 of the experiment and on the back and rump region from week 12. The IR thermography assessment of the feather damage revealed differences between hens kept in different housing systems in agreement with the feather scoring. In conclusion, it was demonstrated that the IR thermography is a useful tool for the assessment of poultry feather cover quality that is not biased by the subjective component and provides higher precision than feather damage scoring.