The behaviour of all animals is governed by the connectivity of neural circuits in the brain. Neurodevelopmental and neurodegenerative diseases, as well as traumatic injuries to the nervous system, can alter or disrupt the normal connectivity of the brain and result in disability. In this review, we highlight the contributions of the genetic model organism Drosophila melanogaster to our understanding of neural connectivity in health and disease. In this context we also discuss the research areas in which we believe the fruitfly is likely to be a useful model system in the future.