In this study we compare different diagnostic methods to measure HER-2/neu gene amplification in breast cancer with special regard to real-time polymerase chain reaction. Fifty specimens of breast cancer were analyzed, and the use of laser-assisted microdissection prior to PCR was investigated. A total of 38 of 50 cases showed HER-2/neu overexpression in immunohistochemistry. In the 2+ scored group, 2 of 23 cases turned out to be amplified after FISH analysis and 14 of 15 cases in the 3+ group were amplified. Of the 16 amplified cases, 3 initially were measured as nonamplified by real-time PCR but showed amplification after laser capture microdissection. One case showed amplification by PCR but turned out to have only one copy of chromosome 17 by FISH. All 0 or 1+ scored cases were measured as nonamplified both by FISH and PCR. Initial concordance rate between FISH and PCR was 92% and could be increased to 98% using laser-assisted microdissection. FISH and PCR showed high diagnostic accuracy and concordance while immunohistochemistry overestimates amplification within the 2+ scored group. Therefore, either FISH or PCR should be applied in cases scored 2+ by immunohistochemistry. Diagnostic accuracy of PCR can be increased using laser-assisted microdissection.