Biosilica from diatoms is formed at ambient conditions under the control of biological and physicochemical processes. The changes in growth and biosilica formation through uptake of different concentrations of Cd2+ by the diatom Nitzschia palea (Kutzing) W. Smith was investigated, correlating Cd2+ effects to changes in the biosilica nanostructure and the relative content of the encapsulated biomolecules. Diatom growth rates at different Cd2+ concentrations (as 1, 2, 3, 4, and 5 X 10-1 mg L-1 CdCl2) were studied in order to determine the concentrations at which sublethal effects were visible, allowing the harvest of sufficient diatom cells for further experiments. We found a clear correlation between the Cd2+ concentrations and both the nanostructure of the biosilica and content of encapsulated peptides. Cd2+ induced biosilica deformation was assessed by scanning electron microscopy and attenuated total reflectance-Fourier Transformed Infrared Spectroscopy (FTIR), revealing that micromorphological changes in frustule features (striae, costae, pores) and nanostructural modifications (structure of the silica and conformation of the encapsulated peptides) occurred at applied Cd2+ concentrations of 2 and 3 X 10-1 mg L-1. In particular the FTIR contribution of peptides decreased at elevated Cd2+ concentrations, whereas shifts in wave number of several relevant organic bonds as C = O stretching (1765 cm-1) and possibly hydrated sulfate (1160, 1110 and 980 cm-1) were assigned. Additional analysis of the amide I band showed a relative increase in beta-sheet structure (16801620 cm-1) when Cd2+ concentration increased. Cadmium uptake clearly affected the molecular ordering of the biosilica in Nitzschia palea, most probably by interfering in biological or physicochemical processes involved in diatom biosilicification.