Aims To assess the correlation between macular morphology and visual acuity in retinitis pigmentosa (RP) patients with cystoid macular oedema (CME). Design Retrospective cross-sectional study. Patients and methods Forty-one eyes of 25 RP patients with CME. Patients underwent cross-sectional scans with optical coherence tomography (Stratus OCT). Age, total retinal thickness, photoreceptor thickness, and the transverse and vertical lengths of the cystoid space were measured. Correlation between visual acuity and each of the measurements were examined. Additionally, the status of the inner segment/outer segment junction (IS/OS) was classified as being absent, discontinuous, or distinct. Measurements were then compared among the three groups. Results Total retinal thickness or photoreceptor thickness was not correlated with visual acuity. There was a correlation between the transverse length of the cystoid space and visual acuity, although the correlation coefficient was weak (r ¼ 0.30). The logMAR visual acuity in the IS/OS absent group (0.67±0.43) was worse than that seen in the IS/OS discontinuous (0.22 ± 0.19) or IS/OS distinct groups (0.07 ± 0.16) (Po0.001). Conclusions When monitoring CME associated with RP, the status of IS/OS is the essential parameter that needs to be examined.