Atopic dermatitis is a chronic inflammatory skin disorder that typically develops in childhood and often persists into adulthood. Its multifactorial pathogenesis involves genetic predisposition, epidermal barrier dysfunction, immune dysregulation with a predominance of the Th2 response, and environmental and microbiome-related influences. One of its key genetic contributors is filaggrin deficiency due to gene mutations, which leads to decreased of natural moisturizing factor synthesis and increased stratum corneum permeability. Other significant mechanisms include impaired tight junction integrity and epidermal protease–antiprotease activity imbalance. The immune component of atopic dermatitis is characterized by increased levels of cytokines such as interleukin (IL)-4, IL-13, and IL-31, which contribute to inflammation and further skin barrier impairment. Cutaneous microbiota dysbiosis, particularly overgrowth of Staphylococcus aureus, also plays a crucial role in disease exacerbation. Despite advances in understanding the molecular and cellular mechanisms of atopic dermatitis, its diagnosis remains clinical, with limited use of laboratory biomarkers owing to the lack of universal, sensitive, and specific indicators. This review addresses key aspects of epidermal barrier function, genetic mutations, immune responses, and the role of the skin microbiome. Special attention is given to filaggrin gene mutations and the potential of cytokines and other serological markers as diagnostic and prognostic biomarkers. Analysis identified potential targets for diagnosis and disease severity assessment. However, large-scale studies are required to validate their clinical utility. This is especially relevant in personalized medicine and treatment optimization for patients with atopic dermatitis.