Application of gas chromatography–olfactometry (GC–O) analysis to pumpernickel bread and its intermediate products obtained during the fermentative process allowed for the recognition of 32 key aroma compounds with specific odor notes. Subsequent quantitation using the stable isotope dilution assay (SIDA) and calculation of odor activity values (OAVs) revealed 22 compounds with OAV > 1, with the highest OAV for 3-methylbutanal with a malty odor (6660), 2-methylbutanal with a malty odor (4560), 3-(methylthio)­propanal with a boiled potato odor (2047), 3-hydroxy-4,5-dimethyl-2­(5H)-furanone with a lovage-like odor (1233), dimethyl trisulfide with a cabbage-like odor (475), 2-phenylethanol with a rosy odor (414), β-damascenone with a boiled apple odor (200), 4-hydroxy-3-methoxybenzaldehyde with a vanilla-like odor (184), 4-hydroxy-2,5-dimethyl-3­(2H)-furanone with a caramel odor (172), and phenylacetladehyde with a honey odor (100). The results showed that aroma of pumpernickel bread is mostly formed during baking; however, the fermentation process influences the formation of several compounds, such as ethyl acetate, 2,3-butanedione, acetic acid, 3-methyl-1-butanol, ethyl butyrate, ethyl lactate, ethyl-3-methyl butyrate, ethyl hexanoate, phenylacetaldehyde, and 2-phenylethanol. Furthermore, the addition of functional components, such as malt and wheat fiber, affects the concentration of several key odorants in the final product, such as 2- and 3-methylbutanals, 3-hydroxy-2-methyl-4H-pyran-4-one, and 4-hydroxy-3-methoxybenzaldehyde.