Surfaces are continuously exposed to physical, chemical and biological degradation. Among the biological agents that cause deterioration, microorganisms are of critical importance. This work is part of a research programme for the characterisation of the alterations of the Milan Cathedral (Italy). Four stone samples of the Milan Cathedral were chemically analysed and the microbiological growth assessed. X-ray diffraction (XRD) showed that calcite was always present in each sample and one sample was also characterised by the chemical form of alteration gypsum. Using Fourier Transform Infrared Spectroscopy (FTIR) together with Scanning Electron Microscopy (SEM), it was possible to prove that the samples were consolidated with the synthetic acrylics and epoxy resins. The green-black biological patinas of the specimens were studied using cultivation, microscope observations and a method for single-cell detection. Sampling for fluorescent in-situ hybridisation (FISH), with ribosomal RNA targeted oligonucleotide probes, was also performed using adhesive tapes. The bulk of the prokaryotes were Bacteria but some Archaea were also found. The bacterial cells were further characterised using specific probes for Cyanobacteria, and alpha-, beta-and gamma-Proteobacteria. In addition, black fungi isolated from the stone and the fungi of the standard ASTM G21-96(2002) method were employed to test if the detected synthetic resins could be used as the sole source of carbon and energy. One isolated Cladosporium sp. attacked the freshly dried acrylic resin. Results show that the detected bacteria and fungi can cause severe damage both to the stone monument and its synthetic consolidants.