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 to control one risk factor can exacerbate the risk of another disease. To achieve and maintain good overall herd health, livestock systems and management practices need to simultaneously take into account all of the main health disorders. We aimed to identify the characteristics of systems and practices conducive to good herd health using the Welfare Quality® assessment protocol for cattle. This protocol allows an assessment of the level of health and welfare at the herd level according to the opinion of a selected group of 13 experts from animal sciences. Our objectives were to (i) describe the distribution of dairy herds’ health scores in a representative sample of French dairy cattle herds, and (ii) to investigate systems (housing system, milking system, herd size, breed, farm location) and management practices associated with variations of the overall health score of dairy herds. This protocol was carried out on 130 farms between December 2010 and March 2011. A multivariable analysis of variance (ANOVA) was performed to investigate the factors of variation of the overall health score at the herd level. The overall health scores of the farms in the sample were classified as moderate for the vast majority of farms (95.4%) (mainly due to subclinical mastitis, dystocia and pain induced by disbudding/dehorning) and varied little between farms. Some livestock systems were associated with a higher overall health score: straw yards and milking parlors (P < 0.0001), highland vs. lowland locations (P = 0.013), Montbeliarde rather than Holstein breeds (P = 0.006). Some management practices also were associated with a higher level of health: medium herd average parity (P = 0.03), low proportion of dirty cows (P = 0.002) and low proportion of cows with abnormal body condition (P = 0.04). 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.