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The involvement of cytokines in the aqueous humour is important in the development and progression of diabetic macular oedema (DMO) and macular oedema (MO) due to branch retinal vein occlusion (BRVO-MO). In this study, the concentrations of cytokines in the aqueous humour of eyes with DMO and BRVO-MO were measured and compared.Prospective, observational case series. Aqueous samples were obtained from 18 eyes with DMO (DMO group), 12 eyes with BRVO-MO (BRVO-MO group), and 16 normal eyes (control group). The aqueous levels of cytokines, including interleukin (IL)-2, IL-5, IL-6, IL-8, IL-12p70, IL-13, monocytochemotactic protein-1 (MCP-1), macrophage inflammatory protein-1α (MIP-1α), platelet-derived growth factor-AA (PDGF)-AA, transforming growth factor-α (TGF-α), interferon-γ (IFN-γ), epidermal growth factor, fibroblast growth factor 2 (FGF2) and vascular endothelial growth factor (VEGF), were measured.The aqueous levels of IL-8, MCP-1, PDGF-AA and VEGF were higher, and IL-13 was lower in the DMO group compared with the control group. The aqueous levels of IL-8 and VEGF were higher in the BRVO-MO group than in the control group. Compared with the IL-6 and MCP-1 levels in the BRVO-MO group, those levels were significantly higher in the DMO group. Correlation analyses revealed that IL-8 was positively and IFN-γ was negatively correlated with the severity of MO in the DMO group. In the BRVO-MO group, IL-8 and was positively correlated with severity of MO and retinal ischaemia.DMO and BRVO-MO may differ in terms of pathogenesis because the cytokine concentrations in the aqueous humour differ. The results suggest that the inflammatory reaction may be more activated in DMO than in BRVO-MO, and ischaemic insult may play a central role in the development of BRVO-MO.