Amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) represent the two major forms of motoneuron disease. In both forms of disease, spinal and bulbar motoneurons become dysfunctional and degenerate. In ALS, cortical motoneurons are also affected, which contributes to the clinical phenotype. The gene defects for most familial forms of ALS and SMA have been discovered and they point to a broad spectrum of disease mechanisms, including defects in RNA processing, pathological protein aggregation, altered apoptotic signaling, and disturbed energy metabolism. Despite the fact that lack of neurotrophic factors or their corresponding receptors are not found as genetic cause of motoneuron disease, signaling pathways initiated by neurotrophic factors for motoneuron survival, axon growth, presynaptic development, and synaptic function are disturbed in ALS and SMA. Better understanding of how neurotrophic factors and downstream signaling pathways interfere with these disease mechanisms could help to develop new therapies for motoneuron disease and other neurodegenerative disorders.