Zolpidem (ZOL) and zopiclone (ZPC) are non-benzodiazepine hypnotics, with unique effects on sleep architecture compared with conventional benzodiazepines. The two compounds have different profiles in action to two major subtypes of the GABA-A receptors, therefore different effects on sleep structure may be expected. In the present study, the effects of ZOL (10mg) and ZPC (7.5mg) were compared in nine healthy young male subjects during nine-night sessions, employing a crossover design. Time courses during the sessions were significantly different between the compounds in the ratio (%) of S2 and S1. Compared to the baseline, an increase of S2 and a decrease of S1 and SR were caused by ZPC, not by ZOL. SWS was increased by both ZPC and ZOL. Significant changes by ZOL were found during the first 150-min, while changes by ZPC were mostly observed during the second 150-min. This might be related to their half-lives. ZOL did not affect sleep latency in the morning, while ZPC caused a significant decrease. Subjective sleepiness, however, was not increased in the ZPC or ZOL mornings. It was speculated that difference in the action to the GABA-A receptor subtypes might be related to the differences in the effects on the sleep architecture between the compounds.