Mucins are the principal components of mucus and mucin glycosylation has important roles in defence, microbial adhesion, immunomodulation, inflammation and cancer. Mucin expression and glycosylation are dynamic, responding to changes in local environment and disease. Potentially hundreds of heterogenous glycans can substitute one mucin molecule and it is difficult to identify biologically accessible glyco-epitopes. Thirty-seven mucins, from the reproductive and gastrointestinal (GI) tracts of six species (bovine, ovine, equine, porcine, chicken and deer) and from two human-derived cell lines, were purified. Following optimisation of mucin printing to construct a novel mucin microarray, the glycoprofiles of the whole mucins were compared using a panel of lectins and one antibody. Accessible glycomotifs of GI mucins varied according to species and localisation of mucin origin, with terminal fucose, the sialyl T-antigen and N-linked oligosaccharides identified as potentially important. The occurrence of T-and sialyl T-antigen varied in bovine and ovine reproductive tract mucins, and terminal N-acetylgalactosamine (GalNAc) and sulfated carbohydrates were detected. This study introduces natural mucin microarrays as an effective tool for profiling mucin glyco-epitopes and highlights their potential for discovery of biologically important motifs in bacterial-host interactions and fertility.