Extensive information is available in the literature on the specific risk factors of the main health disorders afflicting dairy cattle herds. However, it remains difficult to manage a herd’s overall health because measures controlling one risk factor can exacerbate the risk of another disease. To achieve good overall health, livestock systems and management practices need to simultaneously consider all of the main health disorders. We aimed to identify the systems and practices conducive to good herd health using the Welfare Quality® assessment protocol: Our objectives were: (1) to describe the distribution of herds’ health scores in a French representative sample; and (2) to investigate systems and practices associated with variations of the overall health score. This protocol was carried out on 130 farms between December 2010 and March 2011. A multivariate analysis of variance was performed to investigate variation factors of the overall health score at the herd level. This score was classified as moderate for the majority of farms (95.4%) (mainly due to subclinical mastitis, dystocia and pain induced by disbudding) and varied little between farms. Some systems were associated with a higher overall health score: straw yards and milking parlors (P<0.001), highland versus lowland locations (P=0.008), Montbeliarde versus Holstein breeds (P=0.07). Some practices also were associated with a higher level of health: medium herd average parity (P=0.01), low proportion of dirty cows (P<0.001) and low proportion of cows with abnormal body condition (P=0.07). These results suggest that some systems contribute to better health and that improvement of health can be obtained in the short term by the modification of routine management practices.