Mid-infrared (MIR) spectroscopy is a powerful tool for characterising the vibrations of molecular bonds and is therefore ideal for label-free detection of chemical species. Recent research into thin-film deposition and etching techniques for mid-infrared materials shows potential for realising miniaturised bedside biosensors for clinical diagnostics exploiting MIR spectroscopy, to replace laboratory based-techniques. However, lack of refractive index information for commonly encountered biological media and analytes hampers optimisation of biosensor performance for maximum sensitivity, especially for devices exploiting evanescent spectroscopy. Here we present refractive index data for human whole blood and several aqueous solutions of general interest to the clinical community: anticoagulants, analgesics and buffers. The refractive indices are generally dominated by the water content of each sample and the whole blood spectra exhibit additional strong features due to protein content. Furthermore, we present a generalised method for extracting complex refractive indices of aqueous solutions in the mid-infrared region using conventional attenuated total reflection Fourier transform spectroscopy (ATR-FTIR) without the need for collimated or polarised incident light, as is required for existing methods.