Evaluating soil geochemical diversity in the Amazon Basin has been a challenge largely because most study sites have been at the edge of the basin and it is difficult to get samples in such a region. Here we show that even among the most weathered soils, physicochemical soil properties express lithology. Our results are based on topsoil samples collected from different locations in minimally disturbed areas in the state of Amazonas, Brazil. Soil properties were measured using methods which are suitable for highly developed soils. The Chemical Index Alteration and Weathering Index of Parker was calculated based on the content of metal(loid)s in soils determined by X-ray fluorescence. Descriptive statistics, Pearson correlation, and Principal Component Analysis (PCA) were performed on data. In general, Amazon rainforest soils are more deeply weathered than soils in other Brazilian biomes and tropical rainforests in Asia and Africa. The high coefficient of variation of metal(loid) contents express pedogenesis and parent material diversity. Correlation analysis indicated that the tri-pentavalent elements are strongly associated with Al and Fe contents in the topsoil. In contrast, mono-divalent elements are correlated with sand and silt fractions. According to PCA, five soil groups with defined geochemical compositions and degrees of weathering could be identified: i) acidic sandy podzolized soils; ii) acidic loamy ferralitic soils with the highest content of tri-pentavalent ions; iii) acidic clayey kaolinitic soils with low metal(loid) contents; iv) acidic loamy kaolinitic soils with low metal(loid) contents; and v) silty neutral 2:1 clay soils. This study is the first effort to analyze the geochemical diversity in Amazon rainforest soils. These data are extremely valuable in determining the geochemical background for these soil types and this region. Geochemical variability can be predicted to some extent by lithology and pedogenesis, which can be applied to define the sampling required in future studies.