Objective: To examine the effects of a probiotic protocol on the incidence and severity of respiratory and gastrointestinal infections in elite rugby union athletes across an international competition season. Associations were also investigated between salivary biomarkers of stress (cortisol, alpha-amylase) and mucosal immunity (secretory(s)-IgA). Design: A double-blind RCT was conducted over 27-weeks, divided into three stages: (1) control period; (2) domestic competition; and (3) international competition. Methods: Athletes were assigned a probiotic (n = 9) or placebo (n = 10) supplement. Ultrabiotic 60™ or placebo was taken with food twice daily for 17 weeks and SB Floractiv™ 250 mg added twice daily during stage three. Results: Five infections were diagnosed by the team sports physician across the 27-weeks, three within the intervention period in athletes randomised to the placebo group. No significant group x time interaction effects for salivary cortisol, alpha-amylase or s-IgA were identified over the 27-week time period, although a significant main effect for group and time was identified for salivary cortisol, alpha-amylase, and s-IgA (p < 0.05 for all). When considering stage, significant differences were identified in stage one with s-IgA lower in the probiotic group (p = 0.015). In stage two and three, salivary cortisol was higher in the probiotic group (p = 0.016 and p = 0.001 respectively), and salivary alpha-amylase was higher in the probiotic group in stage three (p = 0.007). Conclusion: The probiotic protocol used in this study was associated with an increase in salivary alpha-amylase supporting its possible role as a host defence peptide.