The impact of a 12-week training program by elite swimmers on systemic and mucosal immunity was studied prospectively to examine the relationship between changes in immune parameters and the incidence of respiratory illness. Saliva was collected before and after selected training sessions at 2 weekly intervals. There were significant decreases in salivary IgA (p = 0.05) and salivary IgM (p < 0.0001) concentrations after individual training sessions, but no significant changes in salivary IgG or albumin concentrations. Over the 12-week training program there were small but statistically significant increases in pre-exercise concentrations of salivary IgA (p < 0.001), IgM (p = 0.015) and IgG (p = 0.003) and post-exercise salivary IgA (p < 0.001). There were no significant trends over the 12 weeks for any class of serum immunoglobulins but a significant fall in NK-cell numbers (p < 0.001). There were no associations between serum or salivary immunoglobulin levels or NK-cell numbers and upper respiratory tract illness (URTI) during the 12-week program. The data indicated that despite changes in some immune parameters during this final training program prior to competition there were no associations detected with URTI for this cohort of elite swimmers.