Celiac disease (CD) is a life-long inflammatory autoimmune condition of the gastrointestinal tract affecting genetically susceptible individuals. Several autoimmune disorders are more prevalent in patients and their close relatives and that risk is gluten exposure duration related. The most frequent reported CD associated conditions are type 1 diabetes mellitus and autoimmune thyroiditis. Associated autoimmune antibodies are frequent in CD and their first-degree relatives, spanning anti-endocrine, anti-gastrointestinal, anti-nuclear, anti-cytoskeleton and anti-neurological antibodies. More specifically, antibodies against thyroid and the endocrine pancreas, anti-gastric and liver, anti-nuclear constituents, anti-reticulin, actin, smooth muscle, calreticulin, desmin, collagens and bone, anti-brain, ganglioside, neuronal and blood vessel were described in sera of the patients in numerous studies. The common immunogenetic theories for the above associations are: sharing common HLA and non-HLA genes, antigenic mimicry, damage-induced neoantigen exposure, altered intestinal permeability, idiotype network dysregulation and epitope spreading. The CD associated autoantibodies enigma, being an epiphenomenon or pathogenic, remains unresolved and presents a challenging area for future research.