The research and detection of biomarker candidates and their structural information analysis have become clinically important during the last decades. Especially neurodegenerative disorders like Alzheimer's or Parkinson disease are characterized by misfolding of body-own proteins into oligomeric and fibrillar ß-sheet enriched higher-level clusters. According to the detection of specific biomarkers in complex media, enzyme-linked immunosorbent assays (ELISA) demonstrate a high specificity and are sensitive to minute peptide amounts. On the other hand, FTIR spectroscopy has been proved to be quite useful for the detection and analysis of protein secondary structures and conformational changes during disease progression. Particular the attenuated total reflection (ATR) technique has been provided, due to its possibility for surface modification, the selective detection of soluble membrane anchored disease related proteins. Thus, secondary structure analysis of various disease related proteins like Prion Protein (PrP) or Amyloid-beta- (Aß) is achieved. Here, we demonstrate an ATR-FTIR based biosensor that combines the advantages of both ELISA and FTIR. Thus, we achieve the maximum specificity with simultaneous structure sensitivity in one sensor. Thereby disease related proteins like Amyloid-beta or alpha-synuclein were detected in complex solutions like cerebrospinal fluid or blood plasma. The determined secondary structure gave information concerning disease state or progression. However, the immuno-biosensor demonstrates the potential of the FTIR-spectroscopy in the biomedical sector.