Antibiotic therapy, especially in pediatric patients, is often associated with significant modifications of the gut microflora, which can lead to intestinal dysbiosis and influence intestinal physiology and immune system functionality. Herein we report the results from a double blind controlled clinical trial in 77 pediatric patients affected by recurrent airway infections, receiving antibiotic therapy with amoxicillin and clavulanic acid. A group was treated with an oral probiotic preparation composed of Lactobacillus paracasei ssp.paracasei CRL-431, Bifidobacterium BB-12, Streptococcus thermophilus TH-4 and a fructooligosaccharide (FOS) during and after antibiotic therapy for seven days, while the other group received placebo. The study revealed a reduction in the Clostridia population, with a contemporary increase in Bifidobacteria and Lactobacilli in fecal samples in the probiotic group and an increase in the Enterobacteria population in the placebo group. Moreover, there was a decreasing trend in secretory IgA production in the probiotic group. Some relevant, but not statistically significant probiotic supplementation effects were identified.