Brains of developing duck embryos and ducklings were analysed daily by light microscopy after complete serial brain sectioning and lysosome staining (Gallyas technique), providing insight into synaptic degradation and degeneration during short periods of synaptogenesis. Both regional and temporal shifting pattern of lysosome accumulation (LA) in degraded synapses were detected in sensory-motor pathways during the course of development. LA occurred in sensory projections of embryos, and proceeded from forebrain sensory fields toward limbic regions and finally motor projections. LA disappeared from these structures at the age of 4–6 weeks. LA was analysed ultrastructurally in selected sensory, limbic and motor regions indicating that lysosomes selectively accumulated in transient synapses, leaving parts of either pre- or postsynaptic elements untouched. In no case did denervated neurons exhibit any signs of cell death. Apparently, the LA phenomenon seems critical in terms of both irreversible elimination and remodelling of persisting synapses. Thus, neuronal rearrangement mediated by lysosomal degradation, i.e. degeneration of synaptic components, is supposed to be an integral constituent of synaptogenesis during adaptive processes in sensory-motor systems. These results are discussed with regard to developing brain functions during behavioural adaptation of this precocious bird.