Bladder carcinoma represents more than 4% of all cancer diseases in Austria. The histomorphological evaluation is invasive and remains a subjective and time consuming technique. On account of this it is necessary to find novel non-invasive approaches which support the pathologists for histological recognition to identify malignancy at an early stage. In the present study, Fourier transform infrared (FTIR) microscopic imaging was combined with univariate and multivariate data analysis methods to study bladder carcinoma tissue sections in detail. The possibility to collect IR spectra of bladder carcinoma tissue sections employing an optimized analytical protocol is demonstrated. The correlation between FTIR microscopic imaging and the morphological tissue features obtained by histological staining of the sections demonstrated that many histomorphological tissue patterns can be visualized in the colour images. The routine generation of high quality imaging data is enabled because of the combination of FTIR technology and optimized sample preparation techniques. This opens a new quality of spectroscopic analyses of cancerous tissue, allowing exploration of molecular changes associated with the histopathological morphology.