Milk production, fertility, longevity and health records, were extracted from databases of two milk recording organisations in the United Kingdom for the first three lactations of the Holstein–Friesian breed. These included data related to health events (mastitis and lameness), voluntarily recorded on a proportion of farms. The data were analysed to calculate disease incidence levels and to estimate genetic parameters for health traits and their relationships with production and other functional traits. The resulting dataset consisted of 124 793 lactations from 75 137 animals of 1586 sires, recorded in 2434 herds. Incidence of health events increased with parity. The overall incidence of mastitis (MAS) and lameness (LAM), defined as binary traits, were 17% and 16%, respectively. Heritability estimates for MAS and LAM were 0.04 and 0.02, respectively, obtained from repeatability linear sire models. Heritability estimates of mastitis and lameness as count traits were slightly higher, 0.05 and 0.03, respectively. Genetic correlations were obtained by bivariate analyses of all pair-wise combinations between milk 305-day yield (MY), protein 305-day yield (PY), fat 305-day yield (FY), lactation average loge transformed lactation average somatic cell count (SCS), calving interval (CI), days to first service (DFS), non-return at 56 days (NR56), number of inseminations (NINS), mastitis (MAS), number of mastitis episodes (NMAS), lameness (LAM), number of lameness episodes (NLAM) and lifespan score (LS). As expected, MAS was correlated most strongly with SCS (0.69), which supports the use of SCS as an indicator trait for mastitis. Genetic correlations between MAS and yield and fertility traits were of similar magnitude ranging from 0.27 to 0.33. Genetic correlations between MAS with LAM and LS were 0.38 and −0.59, respectively. Not all genetic correlations between LAM and other traits were significant because of fewer numbers of lameness records. LAM had significant genetic correlations with MY (0.38), PY (0.28), CI (0.35), NINS (0.38) and LS (−0.53). The heritability estimates of mastitis and lameness were low; therefore, genetic gain through direct selection alone would be slow, yet still positive and cumulative. Direct selection against mastitis and lameness as additional traits should reduce incidence of both diseases, and simultaneously improve fertility and longevity. However, both health traits had antagonistic relationships with production traits, thus genetic gain in production would be slower.