The MCF-7 cell line demonstrated increased sensitivity to 5-FU subsequent to the simultaneous suppression of the GEN1 and Mus81 genes. Reverse transcription-quantitative polymerase chain reaction and western blot analysis confirmed the silencing of the GEN1 and Mus81 genes by assessing the (A) mRNA and (B) protein expression. (C) The sh-Ctrl-1, sh-Ctrl-2, sh-GEN1, sh-Mus81 and sh-GEN1+sh-Mus81 groups were transfected with 4 µg control plasmid, 8 µg control plasmid, 4 µg sh-GEN1 plasmid, 4 µg sh-Mus81 plasmid and 4 µg sh-GEN1 plasmid + 4 µg sh-Mus81 plasmid, respectively. No significant difference in cell survival was identified between the sh-Ctrl-1 and sh-Ctrl-2 groups and the sh-GEN1 group. In contrast to the suppression of GEN1 alone, MCF-7 cells demonstrated significantly enhanced sensitivity to 5-FU when the GEN1 and Mus81 genes were simultaneously suppressed (P<0.05). *P<0.05. GEN1, flap endonuclease GEN homolog 1; Mus81, MUS81 structure-specific endonuclease subunit; sh-Ctrl; control short hairpin RNA; sh-GEN1, GEN1 short hairpin RNA; sh-Mus81, Mus81 short hairpin RNA; 5-FU, 5-fluorouracil.