A compact multi-spectral imaging system is presented as diagnostic tool in dermatology and neurosurgery. Using an electronically tunable filter, a sensitive high resolution digital camera, 140 spectral images from 400 nm up to 720 nm are acquired in 40 s. Advanced image processing algorithms are used to enable interactive acquisition, viewing, image registration and image analysis. Experiments in the department of dermatology and neurosurgery show that multispectral imaging reveals much more detail than conventional medical photography or a surgical microscope, as images can be reprocessed to enhance the view on e.g. tumor boundaries. Using a hardware-based interactive registration algorithm, multi-spectral images can be aligned to correct for motion occurred during image acquisition or to compare acquisitions from different moments in time. The system shows to be a powerful diagnostics tool for medical imaging in the visual and near IR range.