In this paper, a photon-counting three-dimensional imaging laser detection and ranging (LADAR) system that uses a Geiger-mode avalanche photodiode (GAPD) of relatively short dead time ( $45\mathrm{ns}$ ) is described. A passively Q-switched microchip laser is used as a laser source and a compact peripheral component interconnect system, which includes a time-to-digital converter (TDC), is set up for fast signal processing. The combination of a GAPD with short dead time and a TDC with a multistop function enables the system to operate in a single-hit or a multihit mode during the acquisition of time-of-flight data. The software for the three-dimensional visualization and an algorithm for the removal of noise are developed. For the photon-counting LADAR system, we establish a theoretical model of target-detection and false-alarm probabilities in both the single-hit and multihit modes with a Poisson statistic; this model provides the prediction of the performance of the system and a technique for the acquisition of a noise image with a GAPD. Both the noise image and the three-dimensional image of a scene acquired by the photon-counting LADAR system during the day are presented.