Purpose To investigate the possible differences in choroidal thickness (CT) between non-neovascular (NNV) and neovascular (NV) age-related macular degeneration (AMD). Methods A retrospective, observational chart review of consecutive patients diagnosed with NNV AMD in one eye and with NV AMD in the fellow eye was carried out. NNV AMD was classified into four subgroups according to the Beckman Initiative for Macular Research AMD Classification Committee Meeting. CT was manually assessed using enhanced depth imaging optical coherence tomography from 1500 mm nasal to 1500 mm temporal to the fovea. Parametric and nonparametric tests were used to compare quantitative variables, a ?2 test was used to compare categorical variables and logistic regression was used to evaluate associations of CT with other variables of interest. Results In this study, 322 eyes from 161 patients were included and 102 (63.35%) were female and 59 (36.65%) were male, with a mean age of 80.80 ±8.45 years (range 58-99 years). Mean follow-up was 11.2±10.8 months (range 1-38 months). In NNV AMD eyes, the choroid was significantly thicker in the subfoveal and temporal regions of the macula, if compared with NV AMD fellow eyes. Differences in CT between NNV AMD and NV AMD fellow eyes were higher at earlier stages of NNV AMD. Conclusions Subfoveal and temporal choroid was significantly thicker in NNV AMD compared with NV AMD fellow eyes. There was a significant choroidal thinning at advanced stages of NNV AMD. © 2016 by the BMJ Publishing Group Ltd.