In-cylinder mixture formation and combustion are highly influenced by primary breakup of injected fuel. Experimental investigation of this phenomenon directly at the outlet of a diesel injector requires a specialized transmitted light microscopy technique combined with a constant-pressure flow microscopy vessel. The method allows verification of the existence of an intact jet core for various states of injection and different fuels. The jet core is dominated by axisymmetric surface waves during the initial injection phase. By quantification of the wavelengths and comparison with existing breakup theories, boundary layer instabilities are identified as origin of surface waves. Boundary layer wavelengths are found to be larger for a higher fuel viscosity. An occasionally appearing non-cylindrical helical jet shape is visible during the injector's opening and closing phase. The helical jet shape is directly resulting from the nozzle outlet flow. Inner nozzle effects are found to be responsible for generation of the helical structure. A fuel dependence of the helical structure formation and its breakup could not be proved. Results also prove that fuel is exiting the nozzle even after the injector needle is closed, while air is simultaneously moving into the nozzle orifice.