Nitrate is a chemical compound naturally present in fruits and vegetables. This study aims at assessing the nitrate levels and health risks arising from high consumption of fruits and vegetables in Bangladesh. Sixteen species of fruits and vegetables were examined for nitrates using High-Performance Liquid Chromatography with Photo Diode Array (PDA) detector. Ward's hierarchical cluster analysis was carried out to identify the cluster of tested fruits and vegetables for the nitrate contents. A point estimate of the daily intake was applied to find the health risks that arise due to elevated levels of nitrate in fruits and vegetables. The results show that root and tuber vegetables accumulate significantly higher levels of nitrate in comparison to fruits and fruit vegetables (P < 0.05). In cluster analysis, the nitrate accumulation of fruits and vegetables show four clear clusters contributing to 29.54%, 7.17%, 4.42%, and 58.57% of the total nitrate content in the entire sample. The risk assessment of the Estimated Daily Intake (EDI) and Health Risk Index (HRI) of almost all the tested samples was in the acceptable range, except for radish, thereby indicating the acceptance of risk due to nitrate intake in Bangladesh. As nitrate may have had risk factor for health, during cultivation and storing the product should be properly monitored.