Poor health records and increased levels of haptogobin have been shown to correlate with a poor environment, but there is limited data regarding variation between individual animals. This study was carried out using 78 farrow-to-finish pig farms spread throughout the yearly seasons. Data on housing and management were collected on each farm visit. Pathological findings and blood samples were taken from each pig at slaughter. Ten blood samples were analyzed for Lawsonia intracellularis (PIA), Mycoplasma hyopneumoniae, salmonella, and haptoglobin values (HAP). Descriptive statistics and analysis of variance were used to analyze the data. Pigs from farms ranking higher in housing (space allowance) and management (sanitation, cleaning, disinfection, climatic control, and breeding protocol) scores showed lower HAP levels and had a lower within farm variability. Pigs infected with PIA or who had lung lesions also had higher HAP levels. Fasting before transport was found to be negatively correlated with lung lesions. HAP levels were lower when pigs with lung lesions were fasted. In conclusion, haptoglobin sampling on the slaughter line was determined to be relevant for integrative welfare assessment of slaughter pigs at the individual level and for longitudinal monitoring at the farm level.