Phenomenon of the heart rate variability (HRV) during various meditation techniques has been reported. However, most of these techniques emphasized the skill of slow breathing (<0.15 Hz). This paper reports our study on HRV during meditation which emphasizes inward attention. Inward attention has been an important approach for the Zen-meditation practitioners to enter into transcendental consciousness. Two groups of subjects were investigated, 10 experimental subjects with Zen-meditation experience and 10 control subjects without any meditation experience. We analyzed HRV both in time and frequency domains. The results revealed both common and different effects on HRV between inward-attention meditation and normal rest. The major difference of effects between two groups were the decrease of LF/HF ratio and LF norm as well as the increase of HF norm, which suggested the benefit of a sympathovagal balance toward parasympathetic activity. Moreover, we observed regular oscillating rhythms of the heart rate when the LF/HF ratio was small under meditation. According to previous studies, regular oscillations of heart rate signal usually appeared in the low-frequency band of HRV under slow breathing. Our findings showed that such regular oscillations could also appear in the high-frequency band of HRV but with smaller amplitude.