In this paper, we investigate the determinants of over-education in Japan and evaluate its opportunity costs for university graduates. To this end, we use the REFLEX data. Results reveal that over-education level in Japan is high and it brings an important wage penalty for Japanese workers. Large firm and high occupations point toward a significant reduction in the likelihood of over-education. Results for wage regressions for over-education indicate that Japanese workers who achieve jobs in large organizations will experience 20% increase in their wage due to the firm size and, if over-educated, their increase in wage will remain positive. Results for women are puzzling as there is no significant effect associated with gender.