Pig production in New Zealand has been used as a model for a high productivity livestock system. A wide range of factors that affect profitability and productivity in pig production were reviewed and a number of differences between gnotobiotic and “normal” commercially reared pigs were identified. The subclinical impact of the presence of commensal organisms in an otherwise healthy pig was contrasted with the immunological cost of clinical disease and some of the trade-offs between nutrition, production and immunity identified. The immunological impact of vaccination was examined with particular reference to the effect of vaccination on the foetus, sow milk production and the growth characteristics of the newborn pig. The results of a study that examined the down-stream productivity effects of sow vaccination where multiple or minimal antigen vaccines were used prior to farrowing are listed and discussed. This study concluded that there can be significant financial and productivity effects that result from immune responses in pigs.