Despite the established association between chronic idiopathic/spontaneous urticaria (CIU) and presence of antinuclear antibodies (ANAs), the prevalence of autoimmune comorbidities in this population has not been analyzed. Here, we aim to identify clinical and laboratory manifestations associated with ANA-positive CIU. ANA-positive patients were identified via electronic data capture from the electronic patient record database of Leumit Health care Services (LHS) of Israel. Patient characteristics, medical histories, and details of diagnostic workup, medical treatment, and follow-up were retrieved by performing a chart review of electronic patient records (EPRs). The prevalence of target diseases among ANA+ CIU+, ANA+ CIU-, and ANA- CIU+ patients was calculated. A total of 91 ANA+ CIU+, 3131 ANA+ CIU-, and 478 ANA- CIU+ patients were identified. The ANA+ CIU+ group was characterized by higher prevalence of Sjögren's syndrome (SS)-A 52 antibodies (Ab) (7.7% versus 2.4%; p = 0.008), SS-A 60 Ab (11% versus 2.8%; p = - 0.001), and SS-B Ab (14.3% versus 3.2%; p < 0.001), compared with ANA- CIU+ group. Additionally, ANA+ CIU+ patients were more likely to be diagnosed with thyroid autoimmune diseases, higher C-reactive protein (6.4 ± 10.3 versus 4.1 ± 8.8 mg/L; p - 0.027), and more profound basopenia (0.04 ± 0.09 versus 0.15 ± 0.11 cell/mm3; p < 0.001) than ANA- CIU patients. More ANA+ CIU+ patients were resistant to four-fold standard licensed doses of antihistamines than ANA- CIU+ patients [11 (12.1%) versus 29 (6.1%); p = 0.046]. ANA-positive CIU is characterized by higher prevalence of SS-A 52, SS-A 60, and SS-B antibodies and poorer clinical response to antihistamine medications.