Organotins are among the most common marine pollutants in the world, as they are widely used as antifouling paint on ships and fishing nets. It has been reported that organotin preferentially accumulates in the central nervous system, especially in the retinal neurons of marine organisms including fish. In this study, we investigated the effects of waterborne tributyltin (TBT) on early-stage developing zebrafish (Danio rerio). Below the lethal concentrations, TBT specifically increased the number of apoptotic cells in the retina as well as some cells near trigeminal neurons, detected by terminal transferase-mediated nick-end-labeling staining. Apoptosis peaked at 60 hpf and decreased by 72 hpf, which was associated with macrophage accumulation. Furthermore, the effect of TBT was markedly inhibited by antioxidants, ascorbic acid or trolox. These results suggest that TBT preferentially induces apoptosis in the retinal neuron of developing zebrafish. Oxidative stress may be involved in this toxicological response.