Human embryonic stem (hES) cells require cooperative interactions with each other for their survival. Previously, the size of hES cell clumps has been reported to be an important factor in determining their viability during routine serial passage. However, the effects of seeding density of the hES cell clumps per se have not yet been investigated. Therefore, this study attempted to compare the level of spontaneous differentiation of hES colonies passaged at two different split ratios (1:3 and 1:8) of a single confluent well of a six-well dish. After 7 d of in vitro culture following serial passage, hES colonies were assigned into three grades according to their degree of spontaneous differentiation: (1) Grade A, which was completely or mostly undifferentiated; (2) grade B, which was partially differentiated; and (3) grade C, which was mostly differentiated. Assessment of the degree of spontaneous differentiation was based on morphological observations under bright-field and phase-contrast microscopy, as well as on immunocytochemical staining for the pluripotency markers SSEA-3 and TRA-1–81. We observed that, at a split ratio of 1:3, the percentages of grade A, B, and C colonies were 89.5, 8.8, and 1.7%, respectively. This was significantly different from the corresponding values of 52.7, 31.3, and 16.0%, respectively, obtained at a split ratio of 1:8. Hence, our results indicated that a lower passage density led to a higher degree of spontaneous differentiation of hES colonies.