Respiratory infections are very frequent in children. Bacillus clausii has been demonstrated to exert some immunomodulatory activities and to be safe. We conducted a study to investigate whether B. clausii administration in allergic children with recurrent respiratory infections might modulate cytokine pattern. Ten children (mean age 4.4 yr) attending the nursery school were enrolled at the end of school year (i.e. in the summer). Bacillus clausii spores (Enterogermina): 2 billion spores per vial) were administered at the dosage schedule of two vials a day for 4 wk. A panel of cytokines, including interleukin (IL)-1, IL-3, IL-4, IL-6, IL-8, IL-10, IL-12, interferon (IFN)-gamma, transforming growth factor (TGF)-beta, and tumor necrosis factor (TNF)-alpha, was measured by immunoassay in the fluid recovered from nasal lavage, performed before and after the treatment. Bacillus clausii treatment induced a significant decrease of IL-4 levels (p < 0.01) and a significant increase of IFN-gamma (p < 0.05), IL-12 (p < 0.001), TGF-beta (p < 0.05), and IL-10 (p < 0.05) levels. Other cytokines were not significantly modified. In conclusion, this study shows that the B. clausii may exert immunomodulating activity by affecting cytokine pattern at nasal level in allergic children with recurrent respiratory infections.