We present an automated method for measuring the lineal density of red blood cells (RBCs) in human retinal capillaries using adaptive optics near-confocal ophthalmoscopy (AONCO). The spatiotemporal traces of RBCs flowing in retinal capillaries were extracted from AONCO images, enhanced using the Gabor filter, the vesselness filter, and the Hough transform. A total of 43 capillary segments (each 50 µm long) were analyzed in 12 eyes of 12 subjects, and the measurement error of the automated method was 0.09 cell over 50 µm compared with results obtained by manual counting. Our method provides a tool for assessing RBC spatial distribution in retinal capillaries.