Ensuring hygiene and health protection is one of the basic construction requirements. Such requirements are examined when commissioning new constructions and examining defects in constructions already in use. One substantial defect is biocorrosion which represents a synergistic process with a complex variety of factors. It is caused by biochemical manifestations of various micro-organisms (micromycetes). Micromycetes producing mycotoxins therefore play an important role regarding the so-called 'Sick Building Syndrome' that has become a global problem nowadays. The case study presented here aims to demonstrate the effectiveness of the diagnostic methods used in assessing the presence of micromycetes in a building's internal atmosphere and on the internal surfaces of a construction built using traditional construction methods. The methodology of comparing methods is based on their effectiveness, taking into account the identification of type and intensity of micromycetes presence in the air and on the material surfaces in the monitored areas.