The effect of a daily intake of the probiotic strain Lactobacillus casei Shirota (LcS) on the colonisation of pathogens, specifically streptococci and Staphylococcus aureus, in the nose and throat of healthy human volunteers with low natural killer cell activity, was investigated in a randomised and controlled intervention study. The study consisted of a 2-week run-in phase, followed by a 4-week intervention phase. The probiotic treatment group received a fermented milk drink with LcS, while the placebo group received an equally composed milk drink without the probiotic additive. To isolate potential pathogenic streptococci and Staph. aureus, samples from the pharynx, as well as of both middle nasal meati, were taken, once after the run-in phase and once at the end of the intervention phase. Isolated bacteria were identified as either Staph. aureus and α- or β-haemolytic streptococci in a polyphasic taxonomical approach based on phenotypic tests, amplified ribosomal DNA restriction analysis genotyping, and 16S rRNA gene sequencing of representative strains. Salivary secretory immunoglobulin A (SIgA) was used as marker of protective mucosal immunity to evaluate whether LcS treatment influenced SIgA production. No statistically significant effect could be determined for intervention with LcS on the incidence of Staph. aureus in the nasal space, Staph. aureus in the pharyngeal space or for β-haemolytic streptococci and Streptococcus pneumoniae in the pharyngeal space. Thus, the intervention did not influence the nasopharyngeal colonisation with Gram-positive potential pathogens. Production of salivary SIgA as a potential means of microbiota modulation was also not affected.