This study evaluated the performance of an automated choroid segmentation algorithm in enhanced depth imaging optical coherence tomography (EDI-OCT) images from a longitudinal kidney donor and recipient cohort. We assessed 22 donors and 23 patients with end-stage kidney disease during the course of donating and receiving a kidney transplant, respectively, over a period of 1 year. We assessed choroid thickness and area on EDI-OCT scans and compared our automated measurements to manual ones at the same locations. We estimated associations between measurements of the choroid and markers of renal function (serum urea and creatinine, estimated glomerular filtration rate (eGFR)) using correlation and linear mixed-effects models. There was good agreement between manual and automated measures. Automated measures were more precise because of smaller measurement error, especially with repeated measures over time. Associations with renal function were stronger with automated measures (creatinine P=0.01, eGFR P=0.02) compared to manual ones (creatinine P=0.12, eGFR P=0.06). Significant linear associations were observed between the choroid and urea, creatinine, and eGFR in recipients, and urea in donors. Our automated approach has greater precision than manual measurements. Greater longitudinal reproducibility of automated measurements may explain stronger associations with renal function compared to manual measurements. To improve detection of meaningful associations with clinical endpoints in longitudinal studies of OCT, reducing measurement error should be a priority, and automated measurements help achieve this.