Despite growing interest in the application of atmospheric plasma jets as medical treatment strategies, there has been comparatively little research on the potential genotoxic and cytotoxic effects of plasma jet treatment. In this study, we have employed the cytokinesis block micronucleus cytome (CBMN-Cyt) assay with WIL2-NS B lymphoblastoid cells to test the potential genotoxicity, as well as the cytotoxicity, of toxic species generated in cell culture media by an argon (Ar) plasma jet. Elevated levels of cell death (necrosis) and occurrence of chromosomal damage (micronuclei MN, nculeoplasmic bridge NPBs and nuclear bus, Nbuds) were observed when cells were exposed to plasma jet-treated media. These results provide a first insight into how we might measure the genotoxic and cytotoxic effect of plasma jet treatments (both indirect and direct) in dividing human cells.