Chronic spontaneous urticaria (CSU) is a debilitating inflammatory skin disease with a prevalence of approximately 1% of the population. It is characterised by recurrent itchy wheals and/or angioedema for more than 6 weeks without known triggers leading to a high quality of life impairment. The pathogenesis of CSU remains not fully understood. This study aimed to explore the pathomechanism of CSU beyond mast cells and IgE-dependent histamine release and to identify possible biomarkers for the disease and its treatment. We investigated a patient cohort in the first month of omalizumab treatment regarding the IgE levels and changes of gene and miRNA expression in peripheral blood. The cohort was divided into responders and non-responders (depending on the score of the Urticaria Control Test) and compared to a group of healthy controls. Our messenger RNA and microRNA microarray analyses revealed the greatest changes of expression levels at day 2 after the first omalizumab dose. We identified several genes and miRNAs of interest, most of which have not been described to be linked to CSU so far, underlining, for example, to T cell involvement or even suggesting platelet involvement.