A new type of cell-cultivation system based on photo-thermal etching has been developed for the on-chip cultivation of living cells using an agarose microchamber array. The method can be used to flexibly change the chamber structure by photo-thermal etching, even during the cultivation of cells, depending upon the progress in cell growth. We used an infrared (1064 nm) focused laser beam as a heat source to melt and remove agar gel at the heated spot on a thin chromium layer. The melting of the agar occurred just near the chromium thin layer, and the size of the photo-thermally etched area depended almost linearly on the power of the irradiated laser beam from 2 microm to 50 microm. Thus by using photo-thermal etching with adequate laser power we could easily fabricate narrow tunnel-shaped channels between the microchambers at the bottom of the agar-layer even during cell cultivation. After 48 h of cultivation of nerve cells, the nerve cells in two adjacent chambers made fiber connections through the fabricated narrow tunnel-shaped channels. These results suggest that photo-thermal etching occurred only in the area where an absorbing material was used, which means that it is possible to photo-thermally etch lines without damaging the cells in the microchambers. The results also suggest that the agar-microchamber cell cultivation system in combination with photo-thermal etching can potentially be used for the next stage of single cell cultivation including the real-time control of the interaction of cells during cell cultivation.