The present invention relates generally to systems and methods for aligning and implanting orthopedic fixation or stabilization implants within the body. In one embodiment, the system includes at least two bone anchors, at least one of which is provided with an angularly adjustable connector. In one aspect, the system also includes at least one linkage rod, for linking two or more bone anchors through their respective adjustable connectors. The bone anchors and the linkage rod may be locked into place to form a spinal fusion or fixation prosthesis. An alignment tool is provided, for guiding a guidewire through one or more connectors.