This study aimed to investigate the retinal thickness analyser (RTA) as a means to identify the presence of cystoid macular oedema (CMO) in children with uveitis, whether the course of CMO can be monitored using this method, and whether there is a trend towards a correlation between macular oedema and visual acuity (VA) in children. This prospective, cross-sectional study with observer-blinded analysis included 25 eyes. Standardized testing for best corrected distance VA (d-VA), near (reading) VA (n-VA) and slit-lamp examination were conducted. Using the RTA, a 3 x 3-mm scan of the macula was obtained, which was then used to discern CMO and calculate mean foveal thickness (MFT). Macular scanning was possible in all children. Cystoid macular oedema was discerned in 10 eyes (40%) and ruled out in 15. In CMO eyes, d-VA was 0.5 Snellen and n-VA was 2 Jaeger; neither result differed significantly from those in eyes without CMO. Mean foveal thickness correlated with n-VA (r = 0.511, p = 0.015), but not with d-VA (r = 0.271, p = 0.191). After 3 months of tailored therapy, CMO was still detectable in six eyes. Changes in d-VA in the CMO and non-CMO groups were 3 +/- 2.1 and 0.8 +/- 1.8 Snellen, respectively; changes in n-VA were 1 +/- 1.4 and 0.1 +/- 0.3 Jaeger, respectively. Changes in MFT were - 244.8 +/- 137.4 microm and - 0.8 +/- 18.1 microm, respectively. A statistically significant correlation was found between the changes in MFT and n-VA (r = 0.629), but not with that in d-VA (r = 0.292). We used the RTA to establish the presence or absence of CMO according to measurements of the macular region. Our findings show that CMO is a common complication in children with uveitis and can be present even in cases with good d-VA. Mean foveal thickness as measured with the RTA correlates indirectly with n-VA.