ABSTRACT Background Utilization of formalin-fixed, paraffin-embedded (FFPE) archival tissue, which is the most common form of tissue preservation in routine practice, for cytogenetic analysis of microarray comparative genomic hybridization (aCGH) remains challenging. We searched for predictive factors of FFPE DNA performance on aCGH analysis. Materials and methods Tumor DNA was extracted from 63 various types of FFPE archival tissues (31 of breast cancer, 24 of lung cancer, and 8 of thyroid tumor) followed by aCGH analysis using high-density oligonucleotide microarray. In two cases, tumor DNA from a matched frozen sample and tumor DNA after whole-genome amplification (WGA) from an FFPE sample were also analyzed. The derivative log ratio spread (DLRSpread) was used as a metric to assess the overall quality of each aCGH result. Results The DLRSpread was significantly correlated with the double-stranded DNA ratio of tumor DNA, storage time, and degree of Cy5 labeling (P Conclusions The double-stranded DNA ratio of tumor DNA predicted the performance of DNA from FFPE samples on aCGH analysis. Quality control by these metrics can utilize valuable FFPE archival tissue on aCGH analysis. Disclosure All authors have declared no conflicts of interest.