The dust mite Lepidoglyphus destructor is the dominating source of allergens giving rise to asthma and rhinitis among farmers. In a previous study of the localization of allergens in L. destructor we demonstrated that the 39 kDa allergen is associated with digestion. Here we describe the localization of the principal 15 kDa allergen and the high molecular weight allergen complex (79 and 93 kDa) in L. destructor with confocal laser scanning microscopy (CLSM). Cryostat-cut sections of mite bodies and faecal pellets were probed with mouse monoclonal antibodies (MoAbs) raised against the allergens. The 15 kDa allergen disclosed labelling of the mite body and most of the faecal pellets but left the exoskeleton unlabelled. The binding was widespread, and most intense in the mouth region. However, some staining was also observed around the gastrointestinal tract. In contrast, the 79 and 93 kDa allergen complex stained the exoskeleton and the front part of the mile. Interestingly, we detected no labelling of the faecal pellets with the MOAb against the 79/93 kDa allergen. The study indicates that the 15 kDa allergen is associated with the digestive tract whereas the function of the 79 and 93 kDa allergen complex remains to be elucidated.