In this paper, a heart rate variability analysis system is presented for short-term (5 min) applications, which is composed of an electrocardiogram signal acquisition unit and a heart rate variability analysis unit. The electrocardiogram signal acquisition unit adopts various digital technologies, including the low-gain amplifier, the high-resolution analog-digital converter, the real-time digital filter and wireless transmission etc. Meanwhile, it has the advantages of strong anti-interference capacity, small size, light weight, and good portability. The heart rate variability analysis unit is used to complete the R-wave detection and the analyses of time domain, frequency domain and non-linear indexes, based on the Matlab Toolbox. The preliminary experiments demonstrated that the system was reliable, and could be applied to the heart rate variability analysis at resting, motion states. etc.