Background <p>Acute diarrhoea or soft stools can occur in kittens after environmental challenges. The effects of a probiotic on gastrointestinal and immune biomarkers in kittens exposed to three study events were investigated. Healthy weaned 10-week-old kittens were fed a daily dietary supplement of <i>Saccharomyces cerevisiae</i> var. <i>boulardii</i> CNCM I-1079 (SB-1079) or placebo for 7 weeks (20 kittens/group). The study events were a routine booster vaccination (Week 3), a change in housing (Week 5), and a diet transition (Week 6). Outcomes included faecal scores and percentage dry matter (DM%), total serum IgG, faecal IgA, and faecal microbiota. Statistical analyses included Linear Mixed Models and Generalized Linear Mixed Models with group, time and group × time interaction as fixed effects; longitudinal Kruskal-Wallis test corrected for false discovery rate was used for microbiota outcomes.</p> Results <p>Faecal scores were optimal throughout the whole study for 12/20 supplemented kittens vs 8/20 control kittens. Overall, group and group × time did not affect faecal quality or moisture, but in Week 5 (housing change) supplemented kittens had firmer stools (<i>P</i>=0.007) and lower faecal DM% (<i>P</i>=0.032) than placebo kittens. Total serum IgG concentration was affected by group (<i>P</i>=0.028), time (<i>P</i>&lt;0.001) and group × time (<i>P</i>=0.001), and was higher in the probiotic vs placebo group (<i>P</i>&lt;0.039) at Week 7, having increased 250% vs 62% from Week 0. Faecal IgA concentration tended to be higher in the probiotic vs placebo group after booster vaccination (<i>P</i>=0.068). Microbiota composition (weighted Unifrac beta diversity) differed between groups overall (<i>P</i>=0.025), at Week 4 (<i>P</i>=0.017), and in the differences between Week 6 and 7 (<i>P</i>=0.008). In supplemented kittens, relative abundances of Veillonellaceae and Actinobacteria remained stable over the first weeks, and abundance of potential pathogens in the Desulfovibrionaceae family decreased. A decrease in Shannon alpha diversity of faecal microbiota post diet transition was significant in supplemented kittens only (<i>P</i> = 0.008) due to a rapid increase in abundance of the Helicobacteraceae family. </p> Conclusions <p>The impacts of SB-1079 on biomarkers of gastrointestinal and immunological health suggest its potential to promote resilience of these systems in young kittens experiencing physiological challenges like new environments and diet transitions.</p> Clinical trial number <p>Not applicable.</p>