Abstract Egg production faces many challenges of economics, disease control and animal welfare concerns. Therefore, investigation of physiological characteristics in laying hens should be required for further discussion on such issues from a scientific point of view. In this study, we evaluated physiological functions and production parameters of hens raised in three different housing systems, conventional battery cage (CC), enriched cage (EC) and aviary system (AV). Lohmann Selected Leghorn Lite laying hens (n = 251) were used. At first, all the pullets were housed in CC. Then, a telemetric transmitter was implanted to randomly selected 18 hens on d 171 after birth to record electrocardiograms (ECGs), heart rate (HR), body temperature (BT) and locomotor activity (LA). Heart rate variability (HRV), which was analyzed using ECG, has been established as a suitable method for investigating autonomic nervous functions, and to assess stress and well-being of housing systems. On d 200 after birth, some of the hens were randomly selected and transferred to EC or AV (CC; n = 88, EC; n = 72, AV; n = 91), including hens implanted a transmitter (6 hens in each group). All parameters at 10 d before and 1 wk after the group division were compared. Egg laying rate (ELR), feed conversion ratio (FCR) and shell deformation were evaluated for egg production parameters. Hens were basically housed under the same management condition, and a constant light-dark cycle (light-on from 0300 to 1930 h). Feeding was conducted during light-phase, and water was supplied ad libitum. Statistical significance was defined as P < 0.05. Comparing the physiological parameter, HR during dark-phase and LA during light-phase after transferred to EC or AV were greater than those in CC. However, there was no significant difference in HR during light-phase or LA during dark-phase between CC and the other two groups. The high frequency (HF) power of HRV, which reflects parasympathetic nervous function, was high during the dark-phase (7.59 ± 1.56) and low during the light-phase (6.04 ± 0.78) in CC. This diurnal variation disappeared in EC or AV because the HF power during the dark-phase decreased. As for production, ELR, FCR and shell deformation were decreased after moved to AV, which were not found in other two groups after the group division. This study was conducted to clarify the effects of housing systems on the physiological functions and productivity of laying hens, and these results suggest that CC might provide hens with parasympathetic dominance with greater quality of rest in dark-phase, and AV causes the reduction of egg production. However, we cannot completely rule out the possibility that these results are influenced by movement to a different housing system. Therefore, further analysis should be performed to assess the relations between physiological functions, management and egg production.