Mutations in superoxide dismutase 1 (SOD1) are responsible for 20% cases of familial amyotrophic lateral sclerosis (ALS). However, the mechanism of motor neuron degeneration caused by ALS-linked SOD1 mutants is not fully understood. Here, we used novel live cell imaging techniques to demonstrate the subcellular localization of EGFP-fused SOD1 of both wild-type (WT) and ALS-linked mutant forms in the endoplasmic reticulum (ER) and Golgi. The presence of WT and mutant SOD1 species in luminal structures was further confirmed by immunoblotting analysis of microsomal fractions from spinal cord lysates of SOD1 transgenic mice prepared by sucrose density-gradient ultracentrifugation. Chemical cross-linking studies also revealed an age-dependent aggregation of mutant SOD1, but not of WT SOD1, prominently in the microsomal fraction. Cell-free translocation assays provided evidence that monomeric SOD1 is a molecular form that can be translocated into luminal structures in the presence of ATP. Our finding that the ER-Golgi pathway is a predominant cellular site of aggregation of mutant SOD1 suggests that secretion could play a key role in pathogenesis, which is in line with the view that the disease is non-cell autonomous.