Objective: No method exists to measure aniseikonia tolerance in stereoacuity. The brain can compensate for 2%–3% aniseikonia (i.e. 2–3 dioptres of anisometropia) without impairing stereoacuity; however, a substantial proportion of anisometropic patients experience problems caused by disruptions of sensory fusion due to surgically induced aniseikonia. We hypothesized that individual differences in tolerance to aniseikonia exist and sought to develop a method to measure aniseikonia tolerance. Methods: A total of 21 eye-healthy phakic individuals older than 50 years of age and 11 patients awaiting clear lens extraction were included. Patients were tested with best corrected near and distance visual acuity, cover/uncover test, eye dominance test, stereoacuity threshold (TNO test), slit lamp examination and ocular coherence tomography. The stereoacuity threshold was determined with aniseikonia induced by different size lenses ranging from 1% to 9% magnification of both eyes in increments of 1%. The aniseikonia tolerance range (ATR) was defined as the percentage aniseikonia in which the stereoacuity threshold was maintained. Results: We examined 32 patients with a median age of 65 (95% CI: 62–66 years), CDVA better than 6/7.5 (0.1 logMAR), and median near visual acuity better than 6/6 (0.0 logMAR). The median stereoacuity threshold was 60 arcsec (maximum 30, minimum 120). We observed large inter-individual differences in ATR: 6/31 (19%) participants had an ATR of ≤1%, 1/31 (3%) had an ATR of 1-5%, 7/31 (22%) had an ATR of 5-10%, and 17/31 (54%) had an ATR of >10%. Conclusion: We present a reliable method for measuring the amount of aniseikonia that a person can tolerate without impairing stereopsis. We report large inter-individual differences in tolerance of aniseikonia.