OBJECTIVE During the last three decades, fluoride varnishes have been recognised as effective strategies for caries prevention in the young-child population and have contributed to a decrease in its prevalence worldwide. The present study aimed to assess in vitro the level of cytotoxicity and genotoxicity in human primary pulp fibroblasts (DPFs) of two NaF varnishes. METHODS Four experimental assays were carried out (MTS, Mitotracker® system [mitochondrial function and morphology], Live/Dead®, and Comet) to assess the morphology, viability, and genotoxicity of two NaF varnishes (Duraphat® and Clinpro White®, both at two different concentrations). The essays were conducted on cultured pulp fibroblasts, grouped in four experimental and two control groups. Collected data were analysed by one-way ANOVA followed by the post hoc Bonferroni test. RESULTS Some morphological changes of DPFs could be detected after the NaFVs stimulation. Most DPFs incubated in Duraphat (22.6 mg/L) maintained their morphological characteristics, except for a small decrease in cell size and shorter cytoplasmic projections (filopodia); DPFs treated with Clinpro White Varnish (22.6 mg/L) presented a morphology and size similar to the control group. DPFs exposed to Duraphat (113 mg/L) exhibited significant morphological alterations with considerable cell size increases and DPFs treated with Clinpro White Varnish (113 mg/L) showed a slight cell size increase without noticeable morphological anomalies. The Duraphat (22.6 mg/L) and Clinpro White Varnish (22.6 mg/L) groups promoted 31% and 35% cell proliferation, respectively, whereas DPFs proliferation with Duraphat (113 mg/L) decreased up to 59%, and cell proliferation with Clinpro White Varnish (113 mg/L) was similar to that of control. CONCLUSIONS All tested varnishes induced changes in the fibroblastic mitochondria. In general, Duraphat was less biocompatible and caused a change in the number of mitochondria compared to Clinpro White Varnish.