During in vitro culture, embryo density in culture medium affects the developmental competence of the embryo. However, in many cases, it is necessary to culture human embryos individually or in small groups. A microwell provides a single embryo with a microenvironment suitable for its development (diameter, 500 μm; depth, 300 μm; and volume, 0.04 μl). In the present study, the clinical results of a microwell system were compared with those of a microdroplet system, and the clinical validity of the microwell system was considered for routine clinical use. In the microwell system, the percentage of embryos that reached the blastocyst stage and the subsequent clinical pregnancy rate (61.7% and 41.4%, respectively) were slightly higher than those in the microdroplet system (51.8% and 34.5%, respectively). Moreover, the microwell system was suitable for routine clinical use with respect to safety, convenience and commercial availability. In conclusion, the microwell system not only slightly enhanced the developmental competence of the individual embryos and the subsequent clinical pregnancy rate, but also made it possible to follow the course of development of an individual embryo. It may therefore be beneficial for conducting elective single embryo transfer to avoid the risks of multiple pregnancy.