This study investigated the distribution and progression of multifocal choroiditis (MFC) inflammatory lesions in 25 eyes of 20 patients and their correlations with clinical outcomes at 24 months. The distribution of choroiditis inflammatory lesions were evaluated semi-automatically using a dedicated software (Region Finder, Version 1.5.0, Heidelberg Engineering) based on fundus autofluorescence. Final visual acuity significantly improved from 0.4 (SD 0.37) LogMAR to 0.25 (0.30) LogMAR (P<0.001). On multivariate analysis, final visual acuity was significantly positively correlated with baseline visual acuity (Coefficient 0.59, P=0.01). Final visual acuity was not associated with total area of chorioretinal lesions at baseline, number of choroidal neovascularisation (CNV) relapses, location of CNV at baseline, total area and number of chorioretinal lesions at final visit and location of CNV at final visit (P>0.05). The mean area of the retina affected by chorioretinal lesions increased significantly from 2.5 (±4.0)mm2 to 4.6 (±5.8) mm2 (P=0.0002) as did number of chorioretinal lesions from 5.9 (±3.6) to 8.3 (±4.4) (P<0.0001) over the course of the two years despite treatment. The authors concluded that patients with MFC tend to have good prognosis. However, the size of chorioretinal inflammatory foci tend to enlarge despite control of disease.