The development of fluorophores with photoemission beyond 1000 nm provides the opportunity to develop novel fluorescence microscopes sensitive to those wavelengths. Imaging at wavelengths beyond the visible spectrum enables imaging depths of hundreds of microns in intact tissue, making this attractive for volumetric imaging applications. Here, a novel shortwave-infrared line-scan confocal microscope is presented that is capable of deep imaging of biological specimens, as demonstrated by visualization of labeled glomeruli in a fixed uncleared kidney at depths beyond 400 µm. Imaging of brain vasculature labeled with the near-infrared organic dye indocyanine green, the shortwave-infrared organic dye Chrom7, and rare earth-doped nanoparticles is also shown, thus encompassing the entire spectrum detectable by a typical shortwave-infrared sensitive InGaAs detector.