Aim: SNPs may be associated with (side) effects of chemotherapy and may be useful as biomarkers to predict febrile neutropenia. Patients & methods: 187 DNA samples extracted from formalin-fixed paraffin-embedded tissue from patients with stage II/III HER2-negative breast cancer were genotyped. Results: Candidate SNPs were selected and explored for association with febrile neutropenia and/or pathological complete response. TT genotype of 388C>T in FGFR4 (rs351855) had a tendency toward higher incidence of febrile neutropenia during neoadjuvant chemotherapy, compared with the CT (p = 0.383) genotype and compared with the CC genotype (p = 0.068). Conclusion: The TT genotype of 388C>T FGFR4 may be related to incidence of febrile neutropenia during neoadjuvant TAC (docetaxel, doxorubicin, cyclophosphamide) chemotherapy and is possibly useful as a patient-related risk factor when assessing febrile neutropenia risk. Original submitted 23 January 2015; Revision submitted 26 May 2015.