The purpose of this study was to assess the effects of lipid peroxidation with occupational exposure to different types of nanomaterials (NMs). In this cross-sectional study, urine and exhaled breath condensate (EBC) samples were collected from 80 NM-handling workers [30 workers handling nano-titanium oxide (nano-TiO2), 28 handling nano-silicon dioxide (nano-SiO2), 22 handling carbon nanotubes (CNTs)], and 69 controls (office workers) from 2010 to 2012. Urinary 8-isoPGF2α, 2,3 dinor-8-isoPGF2α, PGF2α, and EBC 8-iso PGF2α were measured as lipid peroxidation biomarkers in 2013. A significant positive correlation was found between 8-isoPGF2α, 2,3 dinor-8-isoPGF2α, PGF2α, and total isoprostane in urine. Furthermore, significant positive correlations were noted between EBC 8-iso PGF2α and urinary 2,3 dinor-8-isoPGF2α (Spearman correlation r = 0.173, p = 0.035). Exposure to nano-TiO2 resulted in significantly higher levels of urinary 8-isoPGF2α, 2,3 dinor-8-isoPGF2α and PGF2α, even after controlling for confounding factors. Moreover, significant associations and exposure intensity–response relationships between EBC 8-iso PGF2α and NMs were observed in workers, whether handling nano-TiO2, nano-SiO2, or CNTs. Among them, the significant trends were identified based on the intensity of risk levels. These results provided evidence that exposure to nano-TiO2, nano-SiO2, and CNTs may lead to lipid peroxidation in EBC. For routine biomonitoring purposes, this finding, which came through noninvasive methods, may be useful for workers exposed to NMs. Highlights Data regarding the effects of nano-titanium oxide (nano-TiO2), nano-silicon dioxide (nano-SiO2), and carbon nanotubes (CNTs) on lipid peroxidation in workers are limited. 8-Iso PGF2α in exhaled breath condensate of workers exposed to nanoparticles was higher than that of office workers. Exposure to titanium oxide (TiO2) and silica (SiO2) may lead to lipid peroxidation, as indicated by 8-isoPGF2α, 2,3 dinor-8-isoPGF2α, and PGF2α. Examination of lipid peroxidation in EBC has seems to be a useful technique for noninvasive monitoring of workers exposed to nanoparticles.