Several methods have been developed for the measurement of gene amplification and expression. This study compared different molecular genetic analyses (Southern blot analysis (SBA) and polymerase chain reaction (PCR)) with immunohistochemical (IHC) evaluation of the corresponding protein content. PCR may be used as a semi-quantitative analysis of gene amplification and allows DNA extraction from paraffin-embedded blocks. SBA is more accurate than PCR to measure the exact degree of amplification, but only DNA extracted from frozen or fresh tissue can be used. We examined 23 breast tumors and 16 lung tumors, where the genes HER-1 coding for the epidermal growth factor receptor (EGFR) and HER-2 coding for p185HER-2 were analysed. Furthermore, PCR performed on DNA from frozen tissue was compared to PCR on DNA extracted from paraffin-embedded blocks. The results showed correlation between the different analyses, especially when the gene copy number was highly amplified. Some breast tumors showed moderately increased gene copy number of HER-1 by SBA, but no increased protein content by IHC evaluation. This probably reflects that minor degrees of genetic aberrations are not sufficient to cause major biological disturbances, because regulatory cellular pathways are still operating.