Purpose To investigate axial elongation (AE) and changes in relative peripheral refraction (RPR) in anisomyopic children undergoing orthokeratology (ortho-k). Methods Bilateral anisomyopic children, 7-12 years of age, were treated with ortho-k. Axial length (AL) and RPR, from 30 degrees nasal (N30 degrees) to 30 degrees temporal (T30 degrees), were measured at baseline and every 6 months over the study period. AE, changes in RPR and changes in the interocular AL difference were determined over time. Results Twenty-six of the 33 subjects completed the 2-year study. The AE of the higher myopic (HM) eyes (at least 1.50 D more myopia than the other eye) (0.26 +/- 0.29 mm) was significantly smaller than for the less myopic (LM) eyes (0.50 +/- 0.27 mm; p = 0.003), leading to a reduction in the interocular difference in AL (p = 0.001). Baseline RPR measurements in the HM eyes were relatively more hyperopic at T30 degrees, N20 degrees and N30 degrees (p <= 0.02) and greater myopic shifts were observed at T20 degrees (p < 0.001), T30 degrees (p < 0.001), N20 degrees (p = 0.02) and N30 degrees (p = 0.01) after lens wear. After 2 years of ortho-k lens wear, temporal-nasal asymmetry increased significantly, being more myopic at the temporal locations in both eyes (p < 0.001), while AE was associated with the change in RPR at N20 degrees (beta = 0.134, p = 0.01). The interocular difference in AE was also positively associated with the interocular difference in RPR change at N30 degrees (beta = 0.111, p = 0.02). Conclusions Ortho-k slowed AE in bilateral anisomyopia, with slower growth in the HM eyes leading to a reduction in interocular AL differences. After ortho-k, RPR changed from hyperopia to myopia, with greater changes induced in the HM eyes, and slower AE was associated with a more myopic shift in RPR, especially in the nasal field of both eyes.