This study aimed to explore apple transcriptome changes associated with flesh browning during storage using Illumina RNA sequencing. Samples from a browning-susceptible cultivar (‘Braeburn’) were stored for four months under controlled atmospheres. Based on a visual browning index, the inner and outer cortex of the stored apples was classified as healthy or affected tissue. Over 600 million short single-end reads were mapped onto the reference transcriptome, and differences in the expression profiles between healthy and affected tissues were assessed to identify candidate genes associated with internal browning. Genes related to the energy, lipid, cell wall, redox state and secondary metabolic pathways were induced or repressed in the affected tissues, and the expression levels of several of them were confirmed by real-time quantitative PCR.