Sow batch management systems have become more popular due to advantages in labour planning, piglet batch sizes, all-in all-out practices and health management. The present study investigated the potential health advantages of 10 selected farrow-to-finish pig herds before and after transition from a one week batch management system to a four or five week batch management system. Five different animal categories (gilts, sows, piglets, growers and finishers) were sampled at three time points (T0, T1 and T2) before and after transition to a four or five week batch management system. Different matrices of the animals were collected: blood, nasal swabs and faeces. Several economically important diseases were monitored through serology: Lawsonia intracellularis, Porcine Reproductive and Respiratory Syndrome virus (PRRSv), Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae; and PCR-testing: Pasteurella multocida dermonecrotic toxin (DNT) and Brachyspira species, especially the major pathogenic Brachyspira hyodysenteriae. Following serological analysis, the percentage of positive animals per category and sampling occasion were calculated. Health improvement based on serology was defined as the reduction in the percentage of positive animals for a specific disease in a specified animal category. All samples were negative for P. multocida DNT and B. hyodysenteriae. Little to no improvement could be observed for PRRSv. For L. intracellularis an improvement could be observed in piglets (71%) and growers (56%; P < 0.05). For both of the respiratory pathogens, M. hyopneumoniae and A. pleuropneumoniae, significant improvement was observed in finishers (34 and 24%, respectively). In growers, only M. hyopneumoniae showed a significant improvement (34%). In conclusion, the transition from a one week batch management system to a four or five week batch management system in the present herds resulted in a reduction of the percentage of seropositive animals for three of the monitored economically important diseases: L. intracellularis, M. hyopneumoniae and A. pleuropneumoniae.