The human microbiome is an integral part of the body, playing a crucial role in metabolism, energy homeostasis, the regulation of the immune system, and others. The study aims to examine the effect of probiotic ointment on the qualitative composition of the lesional skin microbiome in patients with atopic dermatitis. The study population consisted of 110 patients aged 20 to 45 years with mild atopic dermatitis (AD). The patients were divided into two groups. One group received four different medications: levocetirizine dihydrochloride, enterosgel, topical Tizol gel, and topical 1% hydrocortisone ointment. The other group received a similar treatment with four different medications: levocetirizine dihydrochloride, enterosgel, topical Tizol gel, and topical probiotic ointment. The treatment period was one month. After treatment, the frequency and intensity of the main AD symptoms significantly decreased. A load of S. aureus fell in the probiotic-treated group from 73.4% to 29.1% (p<.05). In the standard-treated group, the S. aureus load decreased from 78.2% to 43.6% (p<.05). The study found that the standard treatment without probiotics helped to decrease S. aureus colonisation in AD patients by 2.00 times (p<.05), whereas using the probiotic ointment reduced S. aureus colonisation by 3 times (p<.05).