<p>The oat is considered a healthy minor cereal. According to numerous studies, their storage proteins tend to provoke a minimal immune response in people with celiac disease. Avenin peptides could still be a source of potentially risky protein epitopes in oats for celiac patients. This study aimed to quantify the transcription of avenin genes during grain filling in six oat varieties. Field experiments were carried out with two levels of fertilization, and samples were collected at eight sampling points. The amount of avenin transcripts was calculated from transcription profiles for each factor: oat variety, avenin gene type, and fertilization level. Statistically significant differences were found in transcript levels between avenin gene types A, B, C1, and C2. The transcripts of the avenin types C1 and C2 were the most abundant. Higher fertilization levels increased both avenin gene transcription and avenin protein content. Although oat varieties did not differ significantly in the abundance of avenin transcripts across the entire maturation period, differences in the abundance of avenin proteins in matured grain proved to be statistically significant. While the content of avenin gene transcripts measured across the entire grain maturation period in selected oat varieties matched the predicted genes, it did not correlate with the content of avenin proteins in matured seed (<i>r</i> = 0.04). This suggests that post-translational modifications may play a role in this discrepancy.</p>