A three-dimensional (3D) image sensor includes a first substrate having an upper pixel. The upper pixel includes a photoelectric element and first and second photogates connected to the photoelectric element. A second substrate includes a lower pixel, which corresponds to the upper pixel, that is spaced apart from the first substrate in a vertical direction. The lower pixel includes a first transfer transistor that transmits a first signal provided by the first photogate. A first source follower generates a first output signal in accordance with the first signal. A second transfer transistor transmits a second signal provided by the second photogate. A second source follower generates a second output signal in accordance with the second signal. First and second bonding conductors are disposed between the first and second substrates and electrically connect the upper and lower pixels.