ABSTRACT Kernels of the rye cultivars Danko and Halo were milled into white flour and compared with flour of the wheat cultivar Rektor. Flour proteins were extracted stepwise with a salt solution (albumins‐globulins), 60% ethanol (prolamins), and 50% 2‐propanol under reducing conditions (glutelins). The quantification by reversed‐phase HPLC indicated that the extractable proteins of both rye flours consisted of ≈26% albumins‐globulins, 65% prolamins, and 9% glutelins. Compared with wheat flour, rye flours comprised significantly higher proportions of nonstorage proteins (albumins‐globulins) and lower proportions of polymerized storage proteins (glutelins). SDS‐PAGE revealed that the prolamin fractions of rye contained all four storage protein types (HMW, γ‐75k, ω, and γ‐40k secalins), whereas the glutelin fractions contained only HMW and γ‐75k secalins. The quantification of secalin types by RP‐HPLC showed a close relationship between the two cultivars.The γ‐75k secalins contributed nearly half (≈46%) of the total storage proteins, followed by γ‐40k secalins (24%) and ω secalins (17%); HMW secalins (≈7%) were minor components, and 6% of eluted proteins were not identified. The amino acid composition of γ‐40k secalins corresponded to those of γ‐gliadins of wheat, whereas γ‐75k secalins were characterized by higher contents of glutamine and proline. Matrix‐assisted laser desorption/ionization and time of flight mass spectrometry (MALDI‐TOF MS) indicated molecular masses of about 52,000 (γ‐75k) and 32,000 (γ‐40k), respectively. N‐terminal amino acid sequences were homologous with those of wheat γ‐ gliadins except for position 5 (asparagine in γ‐75k and glutamine in γ‐40k secalins) and position 12 (cysteine in γ‐75k secalins). The N‐terminal amino acid sequences of HMW and ω‐secalins were homologous with those of the corresponding protein types of wheat. Gel‐permeation HPLC of prolamin fractions revealed that rye flours contained a significantly higher proportion of ethanol‐soluble oligomeric proteins than wheat flour.