Organic pig farming aims at maintaining a high health and welfare state of the animals through appropriate housing, management and feeding. Better knowledge of health and welfare indicators should help to identify critical points and hence to improve health and welfare as well as performance of organic pigs. This paper describes the health and welfare of organic pigs from 101 farms across six EU countries, using selected animal-based parameters from the Welfare Quality® protocol. Parameters were collected in sows, suckling and weaned piglets in 3 to 20 farms per country. Their assessment was trained before farm visits and inter-observer agreement determined after farm visits. The most prevalent problems identified in sows were thinness (median farm prevalence 18.8 %, range 0–81.0), injuries on the anterior part of the body (15.5 %, 0–66.7), injuries on hind part of body (7.9 %, 0–50), obesity (4.9 %, 0–50.0) and vulva lesions (3.5 %, 0–42.9). In suckling piglets, the median prevalence in terms of groups affected per farm was 0 % for all parameters but ‘> 50 % dirty piglets in group’, for which it was 10 %. Farm prevalence ranged from 0 to 100 % for ‘≥ 1 lame piglet in group’, presence of diarrhoea, and ‘> 50 % dirty piglets in group’. In weaned piglets, the median prevalence in terms of groups affected per farm was 0 % with a range of 0 to 100 % for all parameters. Based on the collected data, body condition, skin and vulva lesions in sows, lameness, diarrhoea and respiratory problems in piglets could be used as management and welfare indicators, with good potential for enhancement through farm improvement schemes like herd health planning. However, some definitions could be improved, especially lameness, diarrhoea and respiratory problems in piglets.