This chapter evaluates consumer preferences for agricultural products with eco-label schemes and discusses effective agricultural policies for increasing the consumption of environmentally friendly agricultural products. Various eco-label schemes have been practiced in Japan to support eco-friendly agriculture. This chapter compares two third-party certified eco-labels and a self-declaration scheme. An online questionnaire and choice experiment are conducted, and mixed logit and latent class logit models are used to consider the heterogeneity of consumer preferences. The interesting results are as follows. First, consumer preferences for eco-labeled agricultural products are heterogeneous. Approximately 61% of consumers highly evaluate third-party certified eco-labels and the self-declaration scheme. Second, the characteristics of consumers with heterogeneous preferences are identified. The consumer group that highly evaluates eco-labels will likely include females, older people, high-income individuals, and those with knowledge about environmentally friendly agriculture and experience purchasing environmentally friendly agricultural products. Third, consumers highly value third-party certified eco-labels compared to the self-declaration scheme. The WTP values for third-party certified eco-labels are about 1.4 to 3.5 times that for self-declarations. Based on the results, the effectiveness of third-party certification eco-labels is emphasized to expand the consumption of environmentally friendly agricultural products, and the potential effectiveness of self-declaration schemes is discussed.