Devices and methods for aligning the components of polyaxial screws are described herein. In one embodiment, an alignment instrument includes an elongate frame having a longitudinal axis and a plurality of connection caps slidably disposed along the elongate frame. Each connection cap can removably couple to a polyaxial screw extension tube and selectively lock relative to the elongate frame such that a distance between the plurality of connection caps and an angular orientation of each connection cap relative to the elongate frame is maintained. The instrument can also include a transverse angle indicator to indicate an angular orientation of the elongate frame in a plane transverse to the longitudinal axis of the elongate frame. The device can, for example, capture the orientation of a plurality of polyaxial screws during spinal surgery such that the screws can be returned to the same orientation after manipulation to correct a spinal deformity, etc.