Isotope ratio mass spectrometry and site-specific natural isotope fractionation-nuclear magnetic resonance were applied to determine the overall carbon isotope ratio (delta13C) and the hydrogen isotope ratios [(D/H)I and (D/H)II] of ethanol, respectively. Ethanol was obtained by distillation of fermented cherry mash from a pot still commonly used in fruit brandy production. Analyses of distillate fractions revealed that the distillation proceeds with a fractionation of ethanol isotopologues. The inverse vapor pressure isotope effect (VPIE) observed for the carbon isotopologues is in accordance with the data reported for distillation of ethanol in spinning band columns. In contrast, the inverse VPIE for hydrogen isotopologues of ethanol observed in spinning band columns could not be confirmed. To investigate whether the observed isotope fractionations might influence the applicability of stable isotope analysis for quality and authenticity assessment of fruit brandies, the collected distillate fractions were recombined to cuts, as is common practice in commercial fruit brandy production. Taking into consideration the limits of repeatability of the method, it could be demonstrated that the isotope fractionations observed do not impair the applicability of stable isotope analysis of the carbon and hydrogen isotopes of ethanol for the authenticity assessment of cherry brandies if the cuts are placed in accordance with common distillers' practice.