We measured the level of VRN-B1 transcripts within near-isogenic lines of Triticum aestivum cultivar 'Bezostaya 1' carrying two VRN-B1 alleles from cultivars 'Saratovskaya 29' and 'Diamant 2' (VRN-B1c and VRN-B1a, respectively). Both lines have similar kinetics of VRN-B1 transcript accumulation at the third to fifth leaf stages. However, quantitative PCR analysis at the third leaf stage showed that the VRN-B1c allele was transcribed 10 times faster than the VRN-B1a allele. The F1 hybrid between the lines is more similar to the line carrying the VRN-B1a allele with regard to the level of VRN-B1 transcription. The difference in the transcript levels of the VRN-B1 alleles appears to be due to the previously identified structural changes in the first intron of VRN-B1c (deletion of 0.8 kb and duplication of 0.4 kb) as compared with VRN-B1a, as no other differences were revealed in the present study. We suggested that the first intron structural changes in the VRN-B1c allele as compared with VRN-B1a result in a higher level of VRN-B1 transcripts and an earlier heading time. We confirmed that the expression of the dominant VRN-1 gene induces transcription of the recessive homoeoalleles, coupled with the reduction of the transcript level of a flowering repressor VRN-2.