A dedicated udder health diagnostic programme was developed and used over a 15-year period in South Africa to analyse milk samples based on microbiological and cytological patterns within various groups and for individual cows and udder quarters in dairy herds. These pathogen-specific analyses are utilised for pro-active improvement and management of udder health in South African commercial dairy herds. The programme acts as a monitoring tool and identifies management areas at risk and individual cows with udder disease and uses both quarter and composite milk samples. Intra-mammary infection (IMI) is a dynamic situation and depending on the time a milk sample is taken, false-negative results may be obtained. A new IMI and an infection that is curing may both have low somatic cell counts (SCCs), masking the true bacterial status. SCC in individual infected udder quarters may differ greatly depending on the causative bacterial species, its pathogenicity, the host immune status and the environmental factors involved. A pathogen-specific udder health approach was followed with repeated herd tests to take account of these udder health dynamics. The results of the herd IMI investigation are applied in practice to assist veterinarians, udder health consultants and managers to make informed and specific detailed decisions at both a herd and on an individual cow basis regarding udder health.