BACKGROUND: The vertebrate retina is composed of five major types of neurons: three excitatory (photoreceptors, bipolar cells and ganglion cells) and two inhibitory (horizontal and amacrine cells). The transcription factor Ptf1a (pancreas transcription factor 1a) is important for the normal development of the inhibitory retinal neurons. RESULTS: Using a transgenic Ptf1a:GFP reporter and in situ hybridization in the zebrafish retina, we show that ptf1a message is transiently expressed in all amacrine and horizontal cells within hours after the terminal division of multipotent progenitors at the apical surface of the retinal neuroepithelium, and remains on as these cells migrate to their final laminar location. The message then shuts off, but we can follow the stable Ptf1a:GFP protein for up to 120 hours post-fertilization. A variety of anatomically and neurochemically distinct subtypes of amacrine cells can already be distinguished at this embryonic time point. CONCLUSION: The timing of Ptf1a expression suggests that it is involved in the very early stages or steps in the differentiation of amacrine cells, which, due to the perdurance of the Ptf1a:GFP, can be seen to rapidly diversify into a large number of subtypes. This work sets the stage for future studies looking at genetic specification of amacrine subtypes.