Purpose: The human epidermal growth factor receptor 2 (HER2) status in breast cancer is important for prognostic prediction and the determination of optimal treatment. Current methods rely on protein expression, as determined by immunohistochemistry (IHC), as well as gene amplification as determined by in situ hybridisation (ISH). We explored whether quantitative droplet digital PCR (ddPCR) can be used for the detection and absolute quantitation of HER2 mRNA. Methods: Digital droplet PCR (ddPCR) was performed for HER2 mRNA on 178 formalin-fixed paraffin-embedded (FFPE) breast cancer specimens. HER2 positive, equivocal and negative cases as defined by standard criteria were included and both core biopsies and tissue sections were assessed. Results: HER2 positive cases contained significantly higher levels of HER2 mRNA (169–1,000,000 copies/µl) by ddPCR compared with equivocal (112–139 copies/µl, p = 0.025) and negative cases (6.2–644 copies/µl. p < 0.001). A continuum of transcript quantity was observed but a cutoff of 490 copies/µl distinguished between HER2 positive and negative cases. Results were consistent between core biopsy and tissue sections. Conclusions: ddPCR can be used to quantify HER2 mRNA transcripts in FFPE breast cancer specimens. Our results highlight the potential of ddPCR on FFPE tissue to be used to accurately quantify HER2 transcripts. Validation in large cohorts will be required to determine a clinically applicable cutoff.