For reclaiming alkali soils, pyrite is often used as an amendment. We studied the removal of Fe and Mn through leaching in columns and their subsequent presence in various forms in the soil after applying pyrite and farmyard manure. A highly alkali soil was treated with three levels each of pyrite (equivalent to 0, 50, and 100% of gypsum requirement), alone and in combination with farmyard manure (0, 12.5, and 25 Mg/ha) and was then leached with distilled water. After being leached, the soil in the columns was used to grow rice plants.The results revealed that a major portion of Fe and Mn applied through pyrite was retained in the soil itself, and only a small fraction was removed through drainage water. The contents of available, reducible, and active forms of iron and exchangeable manganese in the soil increased considerably due to pyrite application. Farmyard manure increased the reducible-Fe content, but had little effect on manganese content of the soil. Pyrite also increased the dry matter accumulation and Mn content of rice plant.