Hyperoxaluria corresponds to an excessive urinary excretion of oxalate anions. Hyperoxaluria may be associated with the presence of calcium oxalate monohydrate crystals in kidney tissue and in some cases may lead to renal failure. In this contribution, a set of ten kidney biopsies corresponding to patients affected by hyperoxaluria from various origins such as primary hyperoxaluria or gastrointestinal disease has been investigated through μFourier transform infrared (FTIR) spectroscopy and Field Emission scanning Electron Microscopy (FE-SEM). The complete set of results indicates that if the deposits are mainly constituted of calcium oxalate monohydrate, some of them are made of calcium phosphate apatite, an observation which underlines the use of physicochemical techniques instead of the classical staining procedures. Moreover, FE-SEM observations clearly show a diversity of the crystallite morphology. Such diversity suggests changes in the composition of the milieu along the nephron and different interactions between calcium oxalate crystals and ions or macromolecules such as osteopontin and/or Tamm–Horsfall protein for example. This approach may help the clinician to understand more deeply the biochemical parameters which determine the formation of calcium oxalate monohydrate crystallites in kidney tissue and define the corresponding etiology.