Compound-specific hydrogen and oxygen isotope analyzes on leaf wax-derived n-alkanes (δ 2 H n-alkane) and the hemicellulose-derived sugar arabinose (δ 18 O ara) are valuable, innovative tools for paleohydrological reconstructions. Previous calibration studies have revealed that δ 2 H n-alkane and δ 18 O ara reflect the isotopic composition of precipitation, but-depending on the region-may be strongly modulated by evapotranspirative enrichment. Since no calibration studies exist for semi-arid and arid Mongolia so far, we have analyzed δ 2 H n-alkane and δ 18 O ara in topsoils collected along a transect through Mongolia, and we compared these values with the isotopic composition of precipitation (δ 2 H p-WM and δ 18 O p-WM , modeled data) and various climate parameters. δ 2 H n-alkane and δ 18 O ara are more positive in the arid southeastern part of our transect, which reflects the fact that also the precipitation is more enriched in 2 H and 18 O along this part of the transect. The apparent fractionation ε app , i.e., the isotopic difference between precipitation and the investigated compounds, shows no strong correlation with climate along the transect (ε 2H n-C29/p = −129 ± 14 , ε 2H n-C31/p = −146 ± 14 , and ε 18O ara/p = +41 ± 2). Our results suggest that δ 2 H n-alkane and δ 18 O ara in topsoils from Mongolia reflect the isotopic composition of precipitation and are not strongly modulated by climate. Correlation with the isotopic composition of precipitation has root-mean-square errors of 13.4 for δ 2 H n-C29 , 12.6 for δ 2 H n-C31 , and 1.2 for δ 18 O ara , so our findings corroborate the great potential of compound-specific δ 2 H n-alkane and δ 18 O ara analyzes for paleohydrological research in Mongolia.