DNA aneuploidy (DA) has been considered as a potential cancer biomarker for a long time. Recently, quick, easy and automated sample preparation procedure for flow cytometric (FCM) DNA ploidy analysis has been developed, properly complying with the guidelines for FCM analysis of DA established by Japan Cytometry Society. Therefore, we have investigated the capability of the new procedure for use in clinical practice, and compared it with a conventional manual procedure using lung tissues. There was no major difference between the new and conventional procedures in DA detection with lung tumor. On the other hand, the new procedure had a higher incidence of “shoulder” formation or large CV of 2C peak in general and false DA peak (pseudo-DA) for non-tumor tissues than the conventional procedure. Overall, these results demonstrate that the new procedure is useful to detect DA and confirm the validity of DA as a cancer marker in clinical settings although improvement is required for suppressing pseudo-DA.