Lou Gehrig’s disease currently affects 30,000 people in the US. TAR DNA-binding protein 43 (TDP-43) is associated with Lou Gehrig’s disease and front temporal dementia. There is a need to find effective treatments for these devastating disorders. A key challenge is identifying critical proteins and pathways that mediate TDP-43 insults. Drosophila models have reliable and easy-to-score phenotype in the eye. Using genetic modifiers expressing human TDP-43, crossing it with a next-generation library of 6,484 RNAi strains to assess the effect of silencing individual targets. Genes that suppressed the eye phenotype were catalogued as pathogenic factors, while those that enhanced were catalogued as potential neuroprotectors. We identified almost 300 modifiers of mutant TDP-43 toxicity in a primary screen. To date, there have been confirmed 100 robust suppressors, 80 enhancers and 20 lethals. In summary, this loss-of function genetic screen has led to the identification of several genes and molecular pathways not previously known to be associated with TDP-43 pathologies. The results will provide novel therapeutic targets to approach the devastating TDP-43 proteinopathies and will reveal which pathways could be targeted for better efficacy.