Introduction: Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease. It is associated with atopy, impaired skin barrier, skin infections and several other comorbidities. Aim: To identify comorbidities and risk factors that influence the severity of AD in children. Material and methods: We performed a cross-sectional study involving 52 children newly diagnosed with AD. The severity of AD was assessed with the SCORing Atopic Dermatitis (SCORAD) clinical tool. Levels of serum tryptase, zinc, selenium, and immunoglobulins A, G, M and E (IgA, IgG, IgM, and total IgE, respectively) were determined as well as allergen-specific E antibodies (IgE) to the most common allergens. DNA samples from venous blood were screened for the most common mutations in the filaggrin gene. Results: The median age of patients was 30 months. The median SCORAD index in patients with atopy was 47.8, compared to 27.2 in non-atopic patients (p < 0.01). We also found a significantly higher median SCORAD of 61.2 in patients with low serum IgM levels compared to 34.9 in patients with normal serum IgM levels (p = 0.03). A history of impetigo was also associated with a higher median SCORAD of 56.2 compared to 34.0 in patients without impetigo (p = 0.01). Conclusions: Patients with AD and sensitisation to common allergens, low levels of IgM or a history of impetigo are at risk for more severe disease and, therefore, need more attention, meticulous skin care, proactive management and treatment of comorbidities, when possible.