The prevalence of HER2 amplification according to the percentage of positively stained cells, of polysomy 17 and their correlation with clinical and pathologic characteristics were retrospectively evaluated in a population of 415 breast cancers where fluorescence in situ hybridisation (FISH) was performed to clarify HER2 status previously determined by immunohistochemistry. Forty-two tumours with intense and complete staining in >50% of cells were selected from the same database as internal controls. Among the 415 cases, 233 tumours were IHC 1+, 168 tumours were 2+ and 14 tumours showed an intense and complete immunostaining in 50% of neoplastic cells. HER2 was amplified in 3/14 (21.4%) tumours with 50% and in 36/42 (85.7%) tumours with >50% of intense stained cells, (p<0.001). Polysomy 17 was detected in 77 tumours (16.85%). It was inversely correlated with the percentage of positively stained cells, but not with amplification. Patients with polysomy 17 and no amplification were significantly more likely to have tumours with favourable biological features when compared with patients with HER2 amplification. Our results suggest that FISH testing should be considered for tumours with 50% positive stained cells and that polysomy 17 without amplification is not associated with poor prognostic features.