There is provided a substrate holder which can absorb a change in the thickness between substrates and can hold a substrate while preventing deflection of the substrate and keeping the amount of compression of a substrate sealing member within a certain narrow range. The substrate holder includes a first holding member and a second holding member, both for detachably holding a substrate by holding a peripheral portion of the substrate therebetween; and a substrate sealing member, mounted to the second holding member, for sealing the peripheral portion of the substrate along a substrate sealing line. The first holding member has a thickness absorbing mechanism which biases the substrate toward the second holding member at positions along the substrate sealing line.