Background <p>Photoperiodic changes in diel cycles of gene expression are pervasive in plants. The timing of circadian regulators, together with light signals, regulate multiple photoperiod-dependent responses such as growth, flowering or tuber formation. However, for most genes, the importance of cyclic mRNA levels is less clear. We analyzed the diel transcriptome of modern cultivated potato, a highly heterozygous autotetraploid. Clonal propagation and limited meiosis have led to the accumulation of deleterious alleles, making tetraploid potato an ideal model system to investigate the conservation of cyclic expression and cyclic genes during artificial selection and clonal propagation.</p> Results <p>Our results indicate that rhythmic alleles of cultivated potato are more highly expressed than non-rhythmic genes and are highly co-expressed not only under diel cycles but also across tissues, developmental stages, and stress conditions. Moreover, the smaller ratio of non-synonymous to synonymous differences within rhythmic versus non-rhythmic allelic groups indicates that cyclic genes, in general, have more conserved core functions than non-cyclic genes. In accordance with this observation, fully rhythmic allelic groups are highly enriched in photosynthesis and ribosome biogenesis genes, which have core functions in plants. Furthermore, we investigated differences in cyclic expression patterns between photoperiods identifying potential regulators for the strong changes in phase of expression of ribosome biogenesis and pathogen response genes. Finally, analyses of genes involved in tuber formation suggests that the regulation of <i>CO</i> gene transcription is not the only factor enabling tuberization under long days in modern cultivated potato.</p> Conclusions <p>This study not only provides high quality diel transcriptomic datasets of cultivated potato but also provides important insight on the role of allelic diversity in rhythmic expression in plants.</p>