Polyglandular autoimmune inflammation accompanies Type 1 diabetes (T1D) in NOD mice affecting organs like thyroid and salivary glands. Whereas commensals are not required for T1D progression, germ-free (GF) mice had a very low degree of sialitis, which was restored by colonization with select microbial lineages. Moreover, unlike T1D, which is blocked in mice lacking MyD88-signaling adaptor under conventional but not under GF housing conditions, sialitis did not develop in MyD88-negative GF mice. Thus, microbes and MyD88-dependent signaling are critically required for sialitis development. The severity of sialitis did not correlate with the degree of insulitis in the same animal, was less sensitive to T1D-reducing diet, but was similar to T1D in microbiota-dependent sexual dimorphism. The unexpected distinction in requirements for the microbiota for different autoimmune pathologies within the same organism is crucial for understanding the nature of microbial involvement in complex autoimmune disorders including human autoimmune polyglandular syndromes.