Assessment of occupational exposure to airborne endotoxins was studied for several years but still different procedures are used for sampling and analysis. Among analytical methods LAL test is the most used. A different approach is represented by chemical analyses, based on the detection of the β-hydroxy fatty acids, as markers of lipopolysaccharide (LPS). In this study an analytical method using HPLC-MS/MS was applied to quantify the content of β-hydroxy-dodecanoic (3-OH C 12 ) and β-hydroxytetradecanoic (3-OH C 14 ) acids in thirteen Gram-negative bacterial strains. In order to compare biological and chemical results cell suspensions were analyzed also by Kinetic Chromogenic LAL test. The results obtained by HPLC-MS/MS show that three samples did not contain 3-OH C 12 at all, while 3-OH C 14 was measured in a concentration range from 11.1 to 4007.5µg/L. Endotoxin concentration measured by LAL assay was in the range of 10 2 -10 3 µg/L. Pearson's test showed that the sum of fatty acids by HPLC-MS/MS correlates positively with the LAL Test (r= 0.79) confirming that it can be considered a reliable marker of endotoxin contamination. Principal Component Analysis (PCA) confirms above results and provides additional information grouping microorganisms related with each other on the basis of their biochemical features, habitat and disease spectra.