Rare earth (RE) processing is an environmental hazardous operation. Processed minerals often contain radioactive elements like thorium which occur together with the precious RE elements due to their chemical and physical similarities. Environmental contamination with thorium around RE mining and processing sites is an issue of concern, and many incidences of health impact have been reported. Thorium is enriched during different processing steps like flotation or leaching activities. Therefore, thorium-containing waste arising during RE processing needs a careful waste management since contamination, e.g. by dust drift or tailing dam bursts are severe threats for exposed organisms in the environment. The aim of the paper is to summarize the routes of thorium enrichment along RE mining processes along with the environmental impact and to provide suggestions how to manage thorium enriched waste.