Columnar apple trees (Malus x domestica) are an interesting research object for plant breeders as well as molecular geneticists because of their striking growth habit and the fact that it is caused by the presence of a single dominant allele of the Co gene. The phenotype is characterized by nearly absent lateral branching and an unusual thick stem. Since almost nothing is known about the molecular function(s) of this gene, we performed Illumina RNA-seq next generation sequencing to compare the transcriptomes of columnar and non-columnar shoot apical meristems (SAMs). With this approach, we found hundreds of genes to be differentially regulated, even at different sample collection dates. Functional assignment using gene ontology (GO) tools revealed that many of these genes can potentially be associated with the columnar phenotype. There is noticeable evidence that the expression levels of many genes involved in phytohormone synthesis and signaling are changed. Thus, we hypothesize that columnar growth is in part a consequence of a disregulated phytohormone network.