In this paper we present an algorithm for analysing sets of FTIR microscopic images of tissue sections. The proposed approach allows one to investigate sets of many FTIR tissue images both with respect to sample information (variation from image to image) and spatial variations of tissues (variation within the image). The algorithm is applied to FTIR microscopy images of beef loin muscles containing myofibre and connective tissue regions. The FTIR microscopy images are taken of sub-samples from five different beef loin muscles that were aged for four different lengths of time. The images were investigated regarding variation due to the ageing length and due to the homogeneity of the connective tissue regions. The presented algorithm consists of the following main elements: (1) pre-processing of the spectra to overcome large quality differences in FTIR spectra and differences due to scatter effects, (2) identification of connective tissue regions in every image, (3) labelling of every connective tissue spectrum with respect to its location in the connective tissue region, and (4) analysis of variations in the FTIR microscopic images in regard to ageing time and pixel position of the spectra in the connective tissue region. Important spectral parameters characterising collagen and proteoglycan structure were determined.