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To investigate the differences in the progression of diabetic retinopathy (DR) in both eyes of patients with axial anisometropia.A retrospective review was conducted on diabetic patients who had different axial lengths (difference greater than 1 mm) in each eye. The primary objective of this study was to analyze the differences in the progression of DR in both eyes of patients with axial anisometropia. Fundus images (fluorescein angiography and photographs of the fundus covering the Early Treatment Diabetic Retinopathy Study seven fields) were graded using the Early Treatment Diabetic Retinopathy Study DR grading system. Also, the severity of diabetic retinopathy was analyzed based on the axial length and subfoveal choroidal thickness.Thirty-four of 6,963 patients with DR were included after applying the exclusion and inclusion criteria. The mean age was 53.53 ± 12.20 years and duration of diabetes was 9.63 ± 7.73 years. The mean axial length of the longer and shorter eye was 26.21 ± 2.04 mm and 23.21 ± 1.73 mm, respectively (P < 0.001). In shorter eyes, 61.7% (21 of 34) of the eyes had proliferative diabetic retinopathy. In contrast to the shorter eye, only 8 of the longer eyes (8 of 34, 23.5%) had proliferative diabetic retinopathy (McNemar test, P < 0.001). In eyes with thin subfoveal choroidal thickness (<250 µm), the proliferative diabetic retinopathy ratio was significantly lower (P = 0.007).In patients with axial anisometropia, the longer eye had a lower degree of DR progression than the shorter eye. This result showed that elongation of the axial length had a protective effect against the progression of DR without individual confounding factors.