The search for concomitant autoimmune disorders (ADs) in patients with celiac disease is a pressing issue. The study aimed to determine the rate of the carrier state for antibodies (Abs) being the markers of AD development in patients with celiac disease using various immunological approaches. Enzyme-linked immunoassay and hydrogel microarray-based multiplex immunoassay (MI) were used to determine Abs against thyroid peroxidase (TPO), thyroglobulin (TG), glutamate decarboxylase (GAD), pancreatic islet cells (ICA), tyrosine phosphatase (IA2), 21-hydroxylase (P450c21), Castle's intrinsic factor, tissue transglutaminase (TGM2) in blood serum of patients with celiac disease (group 1, n = 27) and healthy individuals (group 2, n = 16). The microarray also enables testing of Abs against interferons (IFN) alpha and omega, interleukin 22. In group 1, Abs against IA2 (30%), TPO (22%), TG (19%), GAD (19%) were detected by the enzyme-linked immunoassay, and in group 2 Abs against IA2 (38%), TPO (19%), GAD (19%) were detected. In group 1, Abs against TPO (11%), TG (11%), P450c21 (4%), IFN-alpha (4%), ICA (4%) were detected using the microarray, and in group 2 Abs against TPO (13%), ICA (13%), TG (6%), IFN-alpha (6%) were identified. No significant differences in the rate of elevated Abs in the groups were revealed (p > 0.05). Patients, in whom the Ab carrier state was established using microarrays, with negative results enzyme-linked immunoassay can develop the delayed ADs, which suggests prognostic value of MI. The lack of significant differences in the rate of elevated Abs in patients with celiac disease and healthy individuals can result from small size of the studied groups and can suggest high prevalence of potential AD forms in these cohorts.