After providing an overview on the state-of-the-art of measuring condensed phase samples by quantum cascade lasers (QCL), this presentation will focus on protein analysis. The qualitative analysis of mid-IR spectra of aqueous protein solutions provides information on the secondary structure elements present in the proteins under study. In this work an external cavity (EC)-QCL was used for performing transmission measurements of different aqueous protein solutions in a CaF2 flow cell with optical paths up to 75 μm. The strong temperature dependence of the ν2-band of water overlapping the amide I absorption band (~1650 cm-1) required a temperature stability of +/-0.005°C. Successful determination of the secondary structures of albumin and β-lacto-globulin was achieved in the low g/L concentration range