Human epidermal growth factor receptor 2 (HER2 gene) and chromosome 17 polysomy are associated with breast cancer prognosis, chemotherapy and hormone therapy. HER2 gene analysis using fluorescence in situ hybridization (FISH) with 4-µm sections assuming a nuclear diameter of 6 µm caused the loss of genetic DNA. Using intact whole nuclei FISH (WNFISH) and thin tissue section FISH (TTFISH), 109 cases of invasive breast cancer were examined to observe correlations among HER2 gene amplification, CEP17 polysomy and the HER2/CEP17 ratio. The results showed significant differences in the mean copy number of HER2 and the HER2/CEP17 ratios between the WNFISH and TTFISH groups. No significant differences were observed in HER2 amplified, equivocal and non-amplified HER2 samples. Thirty-seven cases of CEP17 polysomy and 72 cases of non‑polysomy were detected by WNFISH. Twenty-nine cases of CEP17 polysomy and 72 cases of non-polysomy were detected by TTFISH. Significant differences were observed between the two methods using the McNemar test (P=0.039). In conclusion, detection of chromosome 17 polysomy in breast cancer with fluorescence in situ hybridization using thin tissue sections may cause the loss of CEP17 and HER2 signals.