Abstract The aim of this study was to test three predictions: (1) that a combination of animal-based parameters indicates better health and welfare in broilers from organic versus conventional farms, (2) that broilers from organic farms show less fluctuating asymmetry (FA) than broilers from conventional farms, and (3) that, at the level of the individual bird, the relationship between FA and welfare is negative and strongest in conventional broilers. On 140 slaughter-age birds randomly selected from seven organic and seven conventional flocks in Belgium we measured standardised FA and five conventional animal-based welfare indicators (tonic immobility duration, latency-to-lie, and condition of the foot pad, hock, and breast). The caeca from the birds from four organic and four conventional flocks were removed for assessing the presence of two bacterial pathogens ( Salmonella and Campylobacter) and the concentration of the health-promoting lactic acid bacteria. Finally, the blood serum concentration of the acute phase protein alpha-1-acid glycoprotein (AGP), a non-specific indicator of immunological stress, was determined. Salmonella was found in the caeca content of two (2.5%) birds only (both from the same conventional farm), whereas 44 (55.7%) birds were infected with Campylobacter. The prevalence of Campylobacter, the concentration of lactic acid bacteria, the duration of tonic immobility, and the condition of the breast and foot pad did not differ between both production systems. Apart from a higher concentration of AGP, organic birds had better scores for hock condition and a longer latency-to-lie indicating better leg health. In addition, organic birds scored better on the aggregated welfare index (i.e. the average of the five standardised welfare indicators). As both production systems differed in many aspects (e.g. slower-growing genotypes, slaughter age, feed, stocking density, group size) it is impossible to assign differences in welfare/health indicators to a single factor. Whatever the causes may be our findings suggest that, despite the potentially elevated risk of immunological challenge, broiler chicken welfare is generally superior in organic farms as compared with conventional farms in Belgium. Regarding the validity of FA as welfare indicator, the prediction of lower FA in the population with highest aggregated welfare score was confirmed but, at the level of the individual, no associations between FA and the aggregated welfare index were found irrespective of whether data from organic and conventional broilers were analysed separately or combined.