Recently, it has been shown that androgen and androgen receptor (AR) also have an important role in the pathogenesis and outcome of breast cancer. However, their significance in different subtypes of breast cancer is still under investigation. The aim of this study was to study the effects of AR on clinicopathological features and prognosis in patients with estrogen and progesterone receptor (ER/PR)-negative, HER2-positive breast cancer. Tumor paraffin-embedded blocks from archives were used for AR study. Data of patients with ER/PR-negative and HER2-positive breast cancer diagnosed at our institute between 1999 and 2010 were recorded and analyzed retrospectively. We studied 36 patients with ER/PR-negative and HER2-positive breast cancer for AR status. Sixteen of them (44.4%) showed AR positivity. The median age was 47 and 56 years for AR-negative and -positive patients, respectively (P = 0.03). The number of postmenopausal patients was higher in the AR-positive than -negative group (56 vs 30%) (P = 0.01). Other demographic data were similar in both group. Histopathological parameters and tumor and nodal stages were similar in both groups. Trastuzumab treatment was more frequently given to AR-positive than -negative patients (94 vs 44%) (P = 0.01). Median follow-up was 47.1 and 34.7 months in AR-negative and -positive groups, respectively (P = 0.03). Relapse occurred in six and four patients in AR-negative and -positive groups. Median progression-free survival (PFS) was similar in both groups (15.7 and 19.6 months in AR-negative and -positive patients, respectively; P = 0.56). Two patients died at 23.4 and 46 months of follow-up in the AR-negative group. There were no deaths in the AR-positive group. Overall survival analyses were not done as a result of an unmet number of events. Median PFS was similar in AR-positive and -negative in that group of patients with ER/PR-negative and HER2-positive breast cancer. However AR-positive patients were more frequently postmenopausal, older, and positive for lymphovascular space invasion. More frequently applied trastuzumab in the AR-positive group might have an effect on the similarity of PFS between the two groups. Studies with higher numbers in this subset of patients with breast cancer will give more robust data.