After harvest potato tubers enter a state of endodormancy. The length of endodormancy is under genetic control and varies between cultivars. Potato tubers can be stored in the endodormant state but application of sprout inhibitors, such as 1,4-dimethylnaphthalene (DMN), are often used to prolong storage. Utilizing transcriptional analysis, we examined changes in gene expression in Solanum tuberosum cv Lamoka tubers during endodormancy and later in storage after tubers transitioned to an ecodormant state. A number of transcripts increased in expression as tubers progressed in storage from the endodormant to the ecodormant state. Abscisic acid and dormancy associated transcripts predominated during the endodormant state and as ecodormancy initiated genes encoding for proteins involved with DNA replication and cell division increased in expression. Treatment of tubers with DMN resulted in an increase in genes associated with stress, wound responses, and DNA methylation. Endodormant tubers treated with DMN exhibited changes in a few hundred transcripts while ecodormant tubers responded with changes in expression of over 3000 genes. The conclusion is that sensitivity of tubers to the sprout inhibitor DMN changed during storage and the sprout inhibitor increased the expression of genes associated with stress.