||Exposure to bacterial endotoxin has been recognized to be associated with various airway inflammation and allergic responses. However, concentrations of airborne endotoxin in the Pearl River Delta Region (PRDR) have not previously been well characterized. Conventional determination of endotoxin concentrations with Limilus Ambocyte Lysate assay suffers from the limitations of significant intra- and inter-laboratory variations in the measured endotoxin levels. A biomarker approach thereby has been proposed as an alternative chemical approach to quantify the level of the total airborne endotoxin. However, the stability of using 3-hydroxy fatty acids (3-OH FAs) as biomarkers for the quantification of airborne endotoxin levels needs to be addressed before this biomarker approach can be applied for the routine measurement of airborne endotoxin levels. In this research, we investigated the stability of 3-OH FAs under different storage and sampling conditions. The results showed that 3-OH FAs were stable at the storage temperatures ranged from -80°C to 4°C and can be stored up to 6 months at -20°C without significant degradation. 3-OH FAs were also highly stable with respect to the sampling temperatures ranged from 15°C to 45°C and the sampling RH ranged from 30% to 90%. However, endotoxins collected at the flow rates of 16.67 L/min and 7.33 L/min resulted in 2.2-fold and 3.6-fold higher concentrations than those collected at 1.13m3/min, respectively. This observation suggests that aerosol samples collected at lower flow rate may lead to overestimated endotoxin levels as a result of bacterial growth during sampling. The high stability of 3-OH FAs adds the advantage of using this biomarker approach for the quantification of airborne endotoxin concentrations in PRDR. Aerosol samples were collected during a one year period from March 2008 to February 2009 in three PRD cities (Guangzhou (GZ), Nansha (NS), and Hong Kong (HK)). The geometric means of endotoxin concentrations in GZ, NS, and HK were 22.32, 16.00 and 13.82 ng/m3, respectively. Furthermore, lower endotoxin levels were observed in summer in the three cities. This was negatively correlated significantly to the ambient temperature as well as relative humidity in Nansha and Hong Kong. Majority of the endotoxins was associated with the PM2.5 or fine particulates in all three cities (GZ: 84%; NS: 70%; HK: 86%) suggesting the ambient endotoxin can potentially deposit deep in human respiratory system. The high occurrence (about 30%) of the odd carbon chain 3-OH FAs in the total endotoxin suggests some source specific bacterial fauna in the region and deserves further investigations. With the high measured endotoxin levels in PRDR, it may possibly pose a chronic health hazard to human.