Since 2014, it has been forbidden to keep pigs outside in Estonia, because of African swine fever. This study compared the welfare and health of pigs raised in indoor conventional and organic systems in Estonia. Selected parameters for comparison were included: stocking densities, behaviour, a human-animal approach test, lameness, dirtiness, tail biting, skin wounds and faecal samples for parasitic egg counts. Organic farms had poorer human-animal interactions compared with conventional farms, but were better in regards to the social and exploratory behaviour among pigs. They were also slightly better regarding lameness and dirtiness compared with conventional farms. Organic farms had less tail biting and skin wounds than conventional farms. Of 16 faecal samples from organic farms, 12 had parasite eggs, while none of the samples from conventional farms were positive. Welfare problems remain to be solved on organic pig farms irrespective of whether they are kept indoors or outdoors, but there are benefits to pig welfare under organic regulations even if they have no access to an outdoor area.