We discuss a hydrogel-free alternate soaking technique for the micropatterning of bioactive ceramics on wettability-patterned substrates around room temperature. Wettability-patterned substrates were fabricated by partly removing self-assembled monolayers on glass plates using mask exposure of UV–Ozone. Hydroxyapatite scaffolds or calcium carbonate films were formed selectively on the hydrophilic surface of the wettability-patterned substrates by alternate soaking of the wettability-patterned substrates in two kinds of calcifying solutions. The wettability-patterned substrates formed with hydroxyapatite scaffolds were immersed in hydroxyapatite precursor for the growth of hydroxyapatite crystals. The c plates of hydroxyapatite crystals were highly aligned parallel to the substrates in the initial stage. This technique allow for the micropatterning of bioactive ceramics with low cost, low energy and short time because this technique does not require bioactive glasses which require calcination process for activation, or hydrogels which need long diffusion time of hydroxyapatite precursor, contributing to the application to templates for bio-living culture cells and cell arrays for medical diagnosis with environmentally-friendly fabrication process in the future.