Microbial exposure has been indicated as significant in the development of asthma and allergy among children. The aim of the study was to test whether microbial exposure and allergens in the school environment are associated with asthmatic symptoms in pupils. Data on asthmatic symptoms and respiratory infections were collected through a questionnaire survey among 1993 pupils aged 11-15 yr in 10 randomly selected schools in Taiyuan, China. Settled dust in classrooms was analysed using tandem gas chromatography-mass spectrometry for 3-hydroxy fatty acids, marker of lipopolysaccharide (LPS) from endotoxin, muramic acid (MuA), marker of bacteria and ergosterol (Erg) for fungi, quantifying both culturable and non-culturable microbes. A total of 29.8% reported daytime attacks of breathlessness, 8.4% wheeze and 1.2% had doctor's diagnosed asthma. Generally, MuA was negatively associated with wheeze and daytime attacks of breathlessness, the latter of which was negatively associated with Erg to a weaker extent. Total concentration of LPS was positively associated with daytime attacks of breathlessness, but shorter lengths of LPS, C10, C12 and C14 LPS were negatively associated with either wheezing or daytime attacks of breathlessness. For MuA and C10 and C12 of LPS, the associations were independent of airborne allergens and classroom crowdedness, and even independent of the other two microbial markers for MuA. Microbial exposure indicated by certain chemical markers (e.g. MuA) could be protective for asthmatic symptoms, but for LPS (endotoxin), the picture is more complex, varying by different lengths of fatty acids of LPS.