Despite advancements in gene editing technologies like CRISPR, the editing process yields heterogeneous populations where some cells have undesired outcomes that bear risk of genome toxicity. These adverse outcomes include the introduction of structural variants, copy number alterations, or chromosomal translocations. Development of efficacious gene therapies hinges on the ability to accurately measure and understand these events. Furthermore, since “cells” are the functional units of gene editing products, it is prudent to measure the co-occurrence of editing results and potential genotoxicity events in a single-cell context. Here, we demonstrate a microfluidics and multiplex PCR based single-cell technology that, in once assay, measures the co-occurrence and zygosity of on-target, off-target edits, translocations between predicted sites, as well as the genomic CNV landscape in over thousands of cells in parallel.