Abstract Background: amyotrophic lateral sclerosis is the most common adult-onset motor neuron disease, characterised by the progressive degeneration of upper and lower motor neurons in the brain and spinal cord. Despite substantial advances in the understanding of underlying disease mechanisms, effective therapies remain lacking. Methods: we generated spinal cord organoids from patient-derived induced pluripotent stem cells and matched isogenic controls to model in vitro the molecular pathology associated with the hexanucleotide repeat expansion within the C9orf72 gene. Results: C9orf72 organoids displayed delayed neuronal maturation, axonal degeneration, mitochondrial abnormalities, enhanced apoptotic signaling, and accumulation of dipeptide repeat proteins. Integrated multi-omics analyses revealed a consistent down-regulation of Netrin-1 at both the transcript and protein levels across patient-derived organoids, suggesting that its loss may contribute to impaired neuronal connectivity, compromised axonal integrity, and increased motor neuron vulnerability in C9orf72 amyotrophic lateral sclerosis. Conclusions: together, these findings establish patient-derived spinal cord organoids as a biologically relevant and in vitro model that recapitulates key cellular and molecular hallmarks of C9orf72-associated amyotrophic lateral sclerosis. This platform provides a valuable framework to deepen disease mechanisms, toward the development of new effective therapeutic strategies.