Objective: The main purpose of this retrospective study was to compare cyclin E expression levels in operable breast cancer patients determined using real-time RT–PCR and immunostaining. The prognostic relevance of cyclin E was also investigated. Methods: Specimens of invasive ductal breast cancer tissues obtained from 124 women during radical mastectomy were analyzed. Results: Of the tumor samples, 40.3 and 59.7% showed high expression of cyclin E in RT–PCR and immunostaining, respectively. The overall agreement probability was 0.032 according to Scott’s p statistic. With a median follow-up of 55.5 months, cyclin E expression assessed using immunostaining was an independent negative prognostic factor in the node positive group(hazardratio3.1;95%CI1.0–9.2;P = 0.045).CyclinEexpressioncorrelatedwithabsence of steroid receptors and younger age. RT–PCR results did not predict survival in any group of patients. Conclusions: Disagreement between real-time RT–PCR and immunostaining was demonstrated. Immunostaining seems to be the more reliable method for assessing cyclin E in breast cancer cells.