A CMOS image sensor includes a pinned photodiode and a transfer gate that are formed using a thick mask that is self-aligned to at least one edge of the polysilicon gate structure to facilitate both the formation of a deep implant and to provide proper alignment between the photodiode implant and the gate. In one embodiment a drain side implant is formed concurrently with the deep n-type implant of the photodiode. After the deep implant, the mask is removed and a shallow p+ implant is formed to complete the photodiode. In another embodiment, the polysilicon is etched to define only a drain side edge, a shallow drain side implant is performed, and then a thick mask is provided and used to complete the gate structure, and is retained during the subsequent high energy implant. Alternatively, the high energy implant is performed prior to the shallow drain side implant.