For in vitro studies, non-toxic doses of nanomaterials are routinely selected by quantification of live cells after exposing to different concentrations of nanoparticles but considering only morphological changes or viability of cells is not sufficient to conclude that these nanomaterials are non-cytotoxic. Here we investigated if secondary toxicity is active in the cells exposed to non-toxic doses of graphene oxide (GO) and graphene quantum dots (GQDs). Non-cytotoxic dose of 15 μg mL-1 of GO (100 nm) and GQDs (50 nm) was selected according to MTT and Hoechst 33342/PI double staining assays. In order to investigate the secondary toxicity, the expression of miR-21, miR-29a and three genes at both mRNA and protein level were evaluated in MCF-7, HUVEC, KMBC/71 cells 4 and 24 h post exposure. Mitochondrial membrane potential (MMP) was assessed by Rhodamine 123 staining. According to our results, there was no significant decrease in viability of cells after exposure to the non-cytotoxic dose of GO and GQDs, but we observed significant alterations in the expression level of miR-21, miR-29a, Bax, Bcl2 and PTEN genes after treatment in all three cells. In addition to molecular changes, we observed alteration in mitochondrial activity at cellular level. However, we also observed that GO influenced the basal level of genes and MMP more compare to GQDs. Considering that all these genes are involved in breast tumor development and metastasis, the observed changes in miRNA expression and protein synthesis may alter cell fate and susceptibility and cause deviation in the desired outcome of GO and GQDs application in medical research.