Salivary glands are frequent sites of manifestations of autoimmune disorders in the head and neck. Sjögren syndrome, sarcoidosis, granulomatosis with polyangiitis, and IgG4-related sialadenitis represent the most important autoimmune salivary gland disorders. Due to the lack of specific symptoms, diagnosis of these conditions remains a challenge. Diagnosis is usually based on classification criteria involving clinical tests, histopathological evaluation, and serological examinations. Depending on the disease, biomarkers are of different value and have to be interpreted carefully. In Sjögren syndrome, antibodies against Ro/SS-A and La/SS-B are essential and part of established classification criteria. In sarcoidosis, biomarkers such as angiotensin-converting enzyme, serum amyloid A, adenosine deaminase, and soluble interleukin-2 receptor are not suitable to confirm a diagnosis due to low sensitivity and specificity, but allow a differentiation between active and inactive disease. In patients with suspected granulomatosis with polyangiitis, positivity for anti-neutrophil cytoplasmic antibodies (ANCA) allows a diagnosis without histopathological confirmation in selected cases. In the head and neck, limited manifestations are common, in which less patients are positive for ANCA and histopathological confirmation is required. Diagnosis of IgG4-related sialadenitis solely based on elevated IgG4 serum levels is not possible. The concentration of blood plasmablasts is reported to have a higher diagnostic value.