The present invention provides an implantable joint prosthesis configured to replace a natural joint, and methods for implantation. The prosthesis may include a first component implantable in a first bone, having a first bearing surface, and a second component implantable in a second bone, having a second bearing surface which corresponds to the first bearing surface. Each bearing surface may include a flattened section such that when the bearing surfaces are placed in cooperation with one another in a preferred orientation, the flattened sections are aligned. Alternatively, the bearing surfaces may have and asymmetric configuration, with non-congruent surfaces that may enable correction of deformity. Several types of implantable joint prostheses are disclosed, including: carpometacarpal, metacarpophalangeal, metatarsophalangeal, distal interphalangeal, proximal interphalangeal, ankle, knee, shoulder, and hip.