Basophil activation test (BAT) is considered to be the best biomarker to predict autoimmune chronic spontaneous urticaria (aiCSU). To date, few studies have investigated the utility of BAT in real-life clinical practice, the role of aiCSU biomarkers in relation to omalizumab therapy and the association between aiCSU tests. This study aimed to analyze the clinical and laboratory features of a prospective cohort with CSU according to their BAT status, as well as to study omalizumab efficacy according to aiCSU biomarkers. A prospective study was conducted from 2010 to 2024 in patients with CSU. BAT alongside other laboratory tests were performed, and clinical and therapeutic features were prospectively collected. Data obtained was compared according to BAT status. Furthermore, omalizumab drug survival was typified according to aiCSU biomarkers. A total of 240 patients were included in the study. BAT positive patients presented more frequently low IgE levels, higher occurrence of IgG anti-thyroid peroxidase (anti-TPO) positivity, autologous serum skin test (ASST) positivity, basopenia, and eosinopenia. The multivariate logistic regression revealed that ASST (OR:7.69, 95%CI: 2.81-21.0) and anti-TPO (OR:2.63, 95%CI: 1.05-6.61) were associated to BAT positivity. All aiCSU biomarkers (BAT, ASST, combined ASST/BAT positivity and low IgE/anti-TPO+) associated significantly shorter omalizumab survival due to failure. In the cohort, both low IgE/anti-TPO+ and ASST were concordant and associated to BAT. The use of BAT in clinical practice delineates a subgroup of patients with specific clinical, laboratory and therapeutic features, including increased omalizumab failure.