A film deposition apparatus to form a thin film by supplying first and second reaction gases within a vacuum chamber includes a turntable, a protection top plate, first and second reaction gas supply parts extending from a circumferential edge towards a rotation center of the turntable, and a separation gas supply part provided therebetween. First and second spaces respectively include the first and second reaction gas supply parts and have heights H1 and H2. A third space includes the separation gas supply part and has a height H3 lower than H1 and H2. The film deposition apparatus further includes a vacuum chamber protection part which surrounds the turntable and the first, second and third spaces together with the protection top plate to protect the vacuum chamber from corrosion.