Background: Diseases such as diabetes have been reported to disrupt circadian rhythms and circadian disruption emerges as an important factor in the prognosis of disease outcomes and treatment success. Our objective was to investigate whether diabetes affects circadian gene expression in endothelial cells and the mechanisms involved in this.  Methods: Induced Pluripotent Stem Cell-Derived Endothelial Cells (iPS-ECs) from healthy and diabetic patients were sequenced and differential analysis was performed. Genes related to circadian rhythms were identified. Primary human retinal endothelial cells (HRECs) were cultured in vivo in hyperglycaemic and hypoxic conditions to validate the results. Cells were synchronised with 50% serum shock and repeated samples collected every 2 hours over a 36 hour period. Circadian gene expression was measured using RT-PCR. Results: ip-ECs from diabetic patients had a 5.7 fold reduction in Dec2 mRNA expression and a 4.0 fold increase in Bmal-2. Synchronised HRECs under hypoxic conditions showed a more robust circadian oscillation but lower amplitude of Bmal-1 and Cry1 mRNA expression, indicating an effect of hypoxia on circadian rhythmicity. Four weeks of hyperglycaemic conditions resulted in a slight increase of Bmal-1 and a reduction in Cry1 and Cry2 mRNA expression. Expression of Dec2 was most affected by hyperglycaemia. Hypoxia had a significant effect in reducing the expression of the majority of circadian genes.  Conclusions: Diabetic conditions resulted in a specific reduction of Dec2 expression in both patient derived iPS-ECs and HRECS in hyperglycaemic conditions. Hypoxia alone had a more pronounced effect on circadian gene expression and rhythmicity compared to hyperglycaemia alone.