Protein adsorption on hydroxyapatite (HAP) thin film was investigated before and after patterning. Hydroxyapatite thin film 100 nm thick was deposited by pulsed laser deposition. The film was patterned by photolithography and wet etching with HCl solution. Proteins (phospholyrase b, bovine serum albumin, and others) labeled with fluorescein isothiocyanate (FITC) were used as the reagent. After the HAP film was soaked in the reagent and washed with pure water, a conspicuous contrast in FITC was observed between the HAP pattern and the glass substrate (or photoresist). This behavior showed that the biocompatibility of the HAP thin film was not influenced by the patterning process. Our technique for HAP thin film is adaptable for applications involving biosensors as electronic devices and scaffolds for tissue culture.