The present invention is related to a Lactobacillus strain, composition and use thereof for treating autoimmune disease and related complications. The composition comprises at least one isolate of Lactobacillus paracasei strain GMNL-32, L. reuteri strain GMNL-89 or L. reuteri strain GMNL-263, and a pharmaceutical carrier, for treating syndromes and related complications of the autoimmune diseases.