We propose to use digital holographic microscopy (DHM) with an illumination in the near infrared spectrum bandwidth, where the silicon is known to have small absorption. With such an illumination condition, it is possible to observe a wider range of specimens than in the visible spectrum, providing a new metrology technique for 3D silicon micro-systems characterization. Suitability of DHM with near infrared illumination for micro-optical elements and wafer inspection is demonstrated. The intrinsic robustness and speed of the method place DHM as a valuable candidate for real-time quality check inside production chains, opening a wide field of applications in quality control.