Confocal laser endomicroscopy provides high potential for noninvasive and in vivo optical biopsy at the cellular level. Here, we report a fully packaged handheld confocal endomicroscopic system for real-time, high-resolution, and in vivo cellular imaging using a Lissajous scanning fiber-optic harmonograph. The endomicroscopic system features an endomicroscopic probe with a fiber-optic harmonograph, a confocal microscope unit, and an image signal processor. The fiber-optic harmonograph contains a single mode fiber coupled with a quadrupole piezoelectric tube, which resonantly scans both axes at similar to 1kHz to obtain a Lissajous pattern. The fiber-optic harmonograph was fully packaged into an endomicroscopic probe with an objective lens. The endomicroscopic probe was hygienically packaged for waterproofing and disinfection of medical instruments within a 2.6-mm outer diameter stainless tube capable of being inserted through the working channel of a clinical endoscope. The probe was further combined with the confocal microscope unit for indocyanine green imaging and the image signal processor for high frame rate and high density Lissajous scanning. The signal processing unit delivers driving signals for probe actuation and reconstructs confocal images using the auto phase matching process of Lissajous fiber scanners. The confocal endomicroscopic system was used to successfully obtain human in vitro fluorescent images and real-time ex vivo and in vivo fluorescent images of the living cell morphology and capillary perfusion inside a single mouse.