In this study, we evaluated the applicability of a flow cytometry-based cytotoxicity (FC) assay previously developed by our laboratory, for monitoring cancer vaccine trials. The assay simultaneously measures effector cell degranulation and target cell death. Clinically relevant samples consisted of frozen peripheral blood mononuclear cells (PBMC) from vaccinated melanoma patients with known response to the melanoma peptide g209. Both PBMC and 7 day in vitro-stimulated lymphocyte from patient samples were used as effector cells in the FC assay. Activity against the relevant g209 and the control g280 peptide measured in the FC assay was directly compared with results obtained from the Granzyme B enzyme-linked immunosorbent spot assay and the standard 51Cr-release assay run in tandem. The FC assay detected low or no activity when PBMC were used as effector cells. Using cytotoxic T lymphocytes as effector cells, little or no effector cell degranulation or cytotoxicity was measured in the FC assay in prevaccination samples. After vaccination, an increase in both degranulation and target cell death could be determined when target cells were pulsed with g209. No or low reactivity was found against g280 at any time point. Our findings exhibited excellent correlation between CD107a expression and GrB secretion and also Annexin V binding to target cells and specific lysis measured in the 51Cr-release assay. Results obtained from the FC assay were highly reproducible. Therefore, the FC assay may be applied to vaccine trial monitoring and allows the measurement of effector cell degranulation and target cell death simultaneously in a single sample.