The connection between the immune response and the composition of gut microbiota has been associated with an increased prevalence of atopic dermatitis in the first year of life. The study aimed to investigate gut microbiota characteristics in infants with atopic dermatitis compared to healthy infants to better understand the link between early-life microbiota composition and the development of atopic dermatitis. The study analyzed the intestinal microbiota of 121 infants with clinical signs of atopic dermatitis, divided into Group I (infants with atopic dermatitis) and Group II (healthy controls). The study showed that infants with atopic dermatitis presented increased values of proteolytic bacteria mainly represented by Enterobacter species (P = 0.041), Klebsiella species (P = 0.038), and Escherichia coli (P = 0.013), with significantly decreased levels of acidifying bacteria represented by Enterococcus species, Lactobacillus and Bifidobacterium (P < 0.05) and normal levels of Clostridium species, Candida albicans, Mould fungi and Geotrichum species. This study highlights distinct differences in the gut microbiota of infants with atopic dermatitis, providing insights into the dynamic intestinal ecosystem during early life for future personalized therapeutic strategies.