This paper considers the influence of thymidylate synthase (TS) and methylenetetrahydrofolate reductase (MTHFR) polymorphisms on the disease-free survival of patients with breast cancer who were treated with adjuvant therapy containing 5-fluorouracil. Relevant clinical data were obtained from the clinical records of 93 patients included in the study. TS and MTHFR genotypes were determined by PCR-agarose gel electrophoresis (TS) and by means of real-time PCR on an ABI PRISM 7000 Sequence Detection System (MTHFR). The median age of 93 patients was 42 years (range 21-76). Fifty patients received CMF, 18 FAC and 25 FEC. The median follow-up of the series was 134 months, with 34 relapses (37%). Sixty patients had a low expression genotype of TS (64.5%) and 33 had a high expression genotype (35.5). No differences in disease-free survival were observed between the two groups (P=0.42). The MTHFR genotype of the 50 patients treated with a chemotherapy regime that included methotrexate was as follows: for C677T, 21 C/C, 21 C/T and eight T/T; for A1298C it was 22 A/A, 24 A/C and four C/C. No differences were found in disease-free survival as regards the MTHFR genotypes (P=0.1 and P=0.6, respectively). Nor were there differences in disease-free survival in the multivariate analyses that included the TS and MTHF genotypes and the relevant clinical variables (P=0.3 for TS, P=0.1 for C677T and P=0.6 for A1298C). This study shows that genotyping the TS or the MTHFR gene is of little value in the individual assessment of the use of adjuvant therapy in breast cancer patients.