Muramic acid (MA) is a unique amino sugar that is a constituent of the peptidoglycan (PG) present in prokaryotic cell walls. MA can serve as a marker for quantifying bacterial load, e.g. in indoor environments, by using gas chromatography-tandem mass spectrometry (GC-MS-MS). We demonstrated recently that the methyl ester O-methyl acetate (MMA) derivative can be used to detect MA in house dust by ion-trap GC-MS-MS. However, since the MMA derivative is not formed from free MA quantification was not optimal. Here we report 1) significant improvements in sample preparation of the MMA derivative and 2) an evaluation of the performance of derivative, using for comparison the alditol acetate derivative, the gold standard in quantitative trace analysis of MA in complex matrices. The MMA derivative was analysed using an MS instrument with internal ionization and the alditol acetate derivative was analysed using an instrument with external ionization. 13C-labelled cyanobacteria, containing MA in their PG, were used as the internal standard. A linear relationship was found between the two methods in studies on 27 parallel samples of airborne dust from school classes collected on filters. Although the analytical sensitivity of the MMA derivatives was somewhat slightly lower than of the alditol acetate derivative, this may be due to differences in yield of derivative, sample clean-up efficiency, or different performance of the GC columns or MS instruments. However preparation of the MMA derivative is quick and compatible with preparation of methyl esters of 3-hydroxy fatty acids (used as markers of Gram negative endotoxin) allowing the levels of both markers to be determined in the same dust sample. In conclusion, the MMA procedure can be used to determine MA in environmental samples with good reproducibility provided the concentration of the 13C-labelled MA internal standard in the cyanobacteria is first determined with an alternative method.