Intrinsically photosensitive retinal ganglion cell (ipRGC) types can be distinguished by their dendritic tree stratification and intensity of melanopsin staining. We identified heavily stained melanopsin-positive M1 cells branching in the outermost part of the inner plexiform layer (IPL) and weakly melanopsin-positive M2 cells branching in the innermost layer of the IPL. A third type can be distinguished by the displacement of the soma to the inner nuclear layer and has morphological similarities with either M1 cells or M2 cells, and is termed here displaced or M-d cells. The aim of the present study was to examine the phenotypic traits of ipRGC types. Using whole retinae from adult mice, we performed immunohistochemistry using melanopsin immunostaining and a number of antibodies directed against proteins typically expressed in retinal ganglion cells. The majority of M1 and M2 ipRGCs expressed Isl-1, microtubule associated protein-2 (MAP2), γ-synuclein, and NeuN, whereas Brn3 transcription factor and the different neurofilaments (NF68, NF160, NF200) were able to discriminate between ipRGC subtypes. Brn3 was expressed preferentially in M2 cells and in a small subpopulation of weakly melanopsin-positive M-d cells with similarities to M2 cells. All three neurofilaments were primarily expressed in large M2 cells with similarities to the recently described alpha-like M4 cells, but not in M1 cells. Expression of NF68 and NF160 was also observed in a few large M-d ipRGCs. These findings show that ipRGCs are not a phenotypically homogenous population and that specific neuronal markers (Brn3 and neurofilament) can partly distinguish between different ipRGC subtypes. J. Comp. Neurol. 521:912–932, 2013. © 2012 Wiley Periodicals, Inc.