Background: With increasing axial length and myopia progression, the micro-structure of the retina and choroid gradually changes. Our study describes the longitudinal changes in retinal and choroidal thickness in school-aged children with myopia and explores the relationship between changes in choroidal thickness and myopia progression. Methods: An exploratory analysis of a randomized trial was performed. Children (n = 168, aged 7 to 12 years) with myopia from − 0.75 dioptre (D) to − 4.00 D were enrolled in this prospective longitudinal study. Cycloplegic refraction, axial length (AL), retinal and choroidal thicknesses were measured at baseline and at 1- and 2-year follow-ups. “Rapid progression myopia” was defined as increasing in myopia > 1.00 D and “stable progression myopia” was ≤ 1.00 D during the 2-year follow-up. Factors affecting the changes in choroidal thickness were analysed using linear mixed models. Results: AL significantly increased by 0.67 ± 0.24 mm with a myopic shift of − 1.50 ± 0.64 D over the 2 years. The overall retinal thickness increased from 251.12 ± 15.91 μm at baseline to 253.47 ± 15.74 μm at the 2-year followup (F = 23.785, P < 0.001). The subfoveal choroidal thickness decreased from 231.03 ± 54.04 μm at baseline to 206.53 ± 59.71 μm at the 2-year follow-up (F = 73.358, P < 0.001). Choroidal thinning was significantly associated with AL elongation (β = − 43.579 μm/mm, P = 0.002) and sex (β = − 17.258, P = 0.001). Choroidal thickness continued to decrease in subjects with rapid progression (F = 92.06, P < 0.001) but not in those with steady progression (F = 2.23, P = 0.119). Conclusion: Significant choroidal thinning was observed and was associated with rapid progression and sex. These findings indicate a need to understand the role of the choroid in eye growth and myopia development. Synopsis/Precis: The macular choroidal thickness of myopic children is relevant to different degrees of myopic progression in this 2-year longitudinal study. These findings suggest that control of choroidal thickness might work to regulate human ocular growth. Trial registration Chinese Clinical Trial Register (ChiCTR): ChiCTR-INR-16007722
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