Human retinal pigment epithelial (RPE) cells at different population doublings (PDs) were cultured for 28 days to examine their phenotypic heterogeneity in a confluent state. In an early population (PD = 2.8), cells showed a cobblestone-like appearance (type I), which gradually became small and tight, and eventually exhibited dark pigmentation. Some cells showed a dome-like structure (type II), which detached from the culture surface during culture. With increasing PD, the cells showed active migration that caused a shift in phenotype from a single layer of large, flattened cells (type III) to a multiple cell layers (stratified) with flattened, irregularly shaped cells (type IV). Immunostaining of specific RPE markers, ZO-1 and Na+/K+-ATPase revealed that cells have markedly decreased expressions in a late population (PD = 10.1). RPE phenotypes were classified into four types by measuring the nuclear size and local density. The frequencies of type I cells decreased with increasing PD value, while the frequencies of type III and IV cells increased along with the decrease in type I. The frequencies of type IV cells at PD = 10.1 had increased by 10.3-fold compared with PD = 2.8. From these results, the nuclear size and local density were proposed as indicators for understanding phenotypic heterogeneity of RPE cells in the passaged cell population during cell expansion. It is concluded that the population doubling level is an important factor to affect the transition of RPE phenotype and thereby to modulate the quality of cultured cells. (C) 2017, The Society for Biotechnology, Japan. All rights reserved.