In the last two decades, an increase in chronic herd health problems of hitherto unknown causes was reported in northwest Germany. For further aetiological clarification, the objective of this project was to reveal differences between herds with good and chronically depressed herd health statuses regarding the symptoms at the herd level. Therefore, a case-control study was conducted. The case farms (case 1 farms: no vaccination against clostridia, n = 45; case 2 farms: multi-clostridia vaccination applied, n = 47) must have fulfilled at least three of the following five criteria: decreased milk yield, increased mortality, increased culling rate, increased number of downer cows, and farmers’ impressions of having herd health problems. The control farms (n = 47) did not fulfil any of these criteria. Multifactorial logistic regression modelling revealed that both types of case farms had fewer overconditioned cows, more cows with skin lesions on their legs, and a lower cow comfort quotient than the control farms. Moreover, the case 1 farms had a longer calving interval, and the cows had more frequently a soiled udder compared to control farms. The case 2 farms had a lower cud chewing index than the control farms. The intraherd prevalences of lameness, cachectic cows and skin lesions were very high compared to recommendations, even on most control farms. These results indicate that different factors, e. g. the housing conditions and management, may play an important role in the presumably multifactorial chronic herd health problems. Therefore, additional aetiological research and veterinary services should consider additional information from all areas of herd management.