The Norwegian dairy goat industry has largely succeeded in controlling caprine arthritis encephalitis (CAE), caseous lymphadenitis (CLA) and paratuberculosis through a voluntary disease eradication programme called Healthier Goats (HG). The aim of this study was to apply an on-farm welfare assessment protocol to assess the effects of HG on goat welfare. A total of 30 dairy goat farms were visited, of which 15 had completed disease eradication and 15 had not yet started. Three trained observers assessed the welfare on 10 farms each. The welfare assessment protocol comprised both resource-based and animal-based welfare measures, including a preliminary version of qualitative behavioural assessments with five prefixed terms. A total of 20 goats in each herd were randomly selected for observations of human–animal interactions and physical health. The latter included registering abnormalities of eyes, nostrils, ears, skin, lymph nodes, joints, udder, claws and body condition score. For individual-level data, robust clustered logistic regression analyses with farm as cluster variable were conducted to assess the association with disease eradication. Wilcoxon rank-sum tests were used for comparisons of herd-level data between the two groups. Goats with swollen joints (indicative of CAE) and enlarged lymph nodes (indicative of CLA) were registered on 53% and 93% of the non-HG farms, respectively, but on none of the HG farms. The only other health variables with significantly lower levels in HG herds were skin lesions (P=0.008) and damaged ears due to torn out ear tags (P<0.001). Goats on HG farms showed less fear of unknown humans (P=0.013), and the qualitative behavioural assessments indicated that the animals in these herds were calmer than in non-HG herds. Significantly more space and lower gas concentrations reflected the upgrading of buildings usually done on HG farms. In conclusion, HG has resulted in some welfare improvements beyond the elimination of infectious diseases. The protocol was considered a useful tool to evaluate the welfare consequences of a disease eradication programme. However, larger sample sizes would increase the reliability of prevalence estimates for less common conditions and increase the power to detect differences between the groups. Despite the obvious link between disease and suffering, this aspect is rarely taken into account in the evaluation of disease control programmes. We therefore propose that welfare assessment protocols should be applied to evaluate the merits of disease control or eradication programmes in terms of animal welfare.