Enzyme immunoassays have been used to detect Helicobacter pylori infection in human body materials such as faeces, urine and saliva. The stool antigen assay (HpSA), which uses polyclonal anti-H. pylori antibody as a capture reagent, has been widely used in the pre-treatment diagnosis of the infection in adults and children. Although the assay has the potential for monitoring eradication therapy, there are controversies over its use, especially at an early stage after treatment. The efficacy of the stool antigen assay can be modified by using monoclonal antibodies towards well characterized H. pylori faecal antigens. Two types of enzyme immunoassays (enzyme-linked immunosorbent assay [ELISA] and immunochromatography) have been used to detect antibodies to H. pylori in urine. Immunochromatography of urine is a rapid assay well suited for epidemiological studies. The salivary ELISA, used in a number of studies, has shown inconsistent results with less than optimum sensitivity and specificity. Urinary and salivary immunoassays may not distinguish between past and present infections, thus limiting their potential to monitor eradication therapy.