The geochemistry of rare earth elements (REEs) was studied in rock samples from host formations, ore samples from two mineral deposits (the Hetaoping Cu-Pb-Zn mine: HTP and the Heiyanao Fe-Cu-Pb-Zn mine: HYA) and the overlying or nearby soils to better understand REE concentrations, distributions and behaviour during weathering from different parent materials at the regional scale, Baoshan area, Yunnan Province, Southwest China. The mudstone and sandstone formations have highest total REE (ΣREE) contents. Chondrite-normalized diagrams for rocks and ores show significant light REEs (LREEs) enrichments and Eu depletion (except for ores in HYA). Cerium displays an obvious negative anomaly in carbonate rocks (Є-3-R, C-R, D-R, T-1-R, and T-2-R). Soils overlying carbonate rock formations (T-1-S, C-S, and Є-3-S) have the highest ΣREE contents, while soils overlying basalts have the lowest ΣREE contents. Soils show enrichments in LREEs with negative Eu anomalies and slight Ce anomalies in the studied soils. Soils with high ∑LREE/∑heavy REE (HREE) values may result from the preferential absorption of LREEs by organic matter. Negative Eu anomalies in soils occur for parent materials in the study area lacking feldspar, especially soils developed from carbonates. Compared to the parent materials, most soils show REE enrichment because alkali metals are removed and REEs are concentrated by low mobility in surficial processes and positive Ce anomalies because of weathering dissolution of other trivalent REEs with ionic radii similar to that of Ca2+.