Endosteal dental implants are used routinely with high success rates to rehabilitate the integrity of the dentition. However if implant surfaces become contaminated by foreign material, osseointegration may not occur and the dental implant will fail because of the lack of mechanical stability. Detection and characterization of dental implant surface contaminants is a difficult task. In this article we investigate the application of several spectral microscopy methods to detect airborne contaminants on dental implant surfaces. We found that Fourier Transform Spectral Imaging Microscopy (FT-SIM) and scanning Raman microscopy provided the most useful information. Some implants possess weak and homogeneous auto-fluorescence and are best analyzed using FT-SIM methods, while others are Raman inactive and can be analyzed using scanning Raman microscopy.