Aims: Amyotrophic lateral sclerosis (ALS) results in the selective loss of motor neurons within several years of disease onset; however, the molecular mechanisms behind ALS pathogenesis remain largely unknown. Among the genes responsible for familial ALS, mutations in TAR DNA-binding protein 43 (TDP-43) have been identified. The present study evaluated the cytotoxicity of TDP-43 fragments and ALS-associated mutants against human embryonic stem cell-derived motor neurons. Methods: Magnetofection was used to investigate the mortality rates of motor neurons after forced expression of TDP-43 C-terminal fragments and ALS-associated TDP-43 missense mutants. Results: Neither wild-type TDP-43 nor the 35-kDa fragment induced cell death. However, the 26-kDa fragment, which forms insoluble aggregates in the motor neurons of ALS patients, showed significant cytotoxicity, similar to mutant forms of TDP-43, including p.A315T and p.A382T. Hence, a motor neuron-specific neurotoxic function might be attributed to both the 26-kDa fragment and the TDP-43 mutants. Thus, 26kDa C-terminal fragment was considered to play an important role in ALS pathology, but alterations in adenosine deaminase acting on RNA 2 (ADAR2) expression, an enzyme accountable for GluA2 (AMPA receptor subunit 2) mRNA editing insufficiency in sporadic ALS, did not lead to alterations in the expression of the 26-kDa fragment. Conclusions: This is the first report showing the influence of specific ALS-associated factors on the mortality of motor neurons through the manipulation of gene expression. The motor neuron disease model described herein might prove useful for the identification of novel pathogenic factors and neuroprotective agents for the treatment of ALS.