To investigate the detectability and expressiveness of salivary and fecal anti-gliadin (AGA), anti-endomysium (EMA) and anti-tissue-transglutaminase (ATA) antibodies, 127 salivary and 160 fecal samples of healthy volunteers and salivary and fecal samples of 17 patients with histologically proven and 9 patients with suggested celiac disease were investigated in this study. With all salivary parameters and fecal IgA AGA, IgM AGA, IgA EMA and IgG EMA, healthy volunteers and patients showed partially overlapping results. The most promising results in our study with higher concentrations in patients with celiac disease were obtained by fecal scIgA AGA and a combined determination of fecal IgA AGA, IgG AGA and IgM AGA. Further investigations should be performed with fecal IgA EMA and scIgA ATA based on human recombinant tissue-transglutaminase. One patient with histologically proven celiac disease had normal serological but high fecal scIgA AGA and scIgA ATA values. This patient emphasizes the importance of fecal antibody determination for the diagnosis of celiac disease, at least in patients with suggested celiac disease and negative serum antibodies.