A simple fabrication method for cell micropatterns on hydrogel substrates was developed using an inkjet printing system that induced hydrogel micropatterns. The hydrogel micropatterns were created from inks resulting in cell-adhesive and non-cell-adhesive printed regions by horseradish peroxidase-catalyzed reaction onto non-cell-adhesive and cell-adhesive hydrogel substrates, respectively, to obtain the cell micropatterns. Cell-adhesive and non-cell-adhesive regions were obtained from gelatin and alginate derivatives, respectively. The cells on the cell-adhesive regions were successfully aligned, resulting in recognizable patterns. Furthermore, the proposed system permits the patterning of multiple cell types by switching the non-cell-adhesive region to the cell-adhesive region in the presence of growing cells. Also, we could fabricate disc- and filament-shaped small tissues by degrading the non-cell-adhesive substrates having dot- and line-shaped cell-adhesive micropatterns using alginate-lyase. These results indicate that our system is useful for fabrication of tailor-made cell patterns and microtissues with the shape defined by the micropattern, and will be conducive to a diverse range of biological applications.