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Objectives The wide use of pesticides raises serious concerns regarding food safety and environmental impacts. There is increasing public concern about the potential health risks linked with exposure to pesticides. Regulation of maximum residue limits (MRL) of pesticide residues in food commodities has been established in many developed countries. For developing countries, like Thailand, this regulation often exists in law, but is not completely enforced in practice. Thus, pesticide residue levels in vegetables and fruits have not been thoroughly monitored. The present study aimed to examine potential health risks associated with pesticide exposure by determining the pesticide residues in two commonly consumed fruits, watermelon and durian. Methods The fruit samples were purchased from markets in central provinces of Thailand and assayed for the content of 28 pesticides. Analysis of pesticides was performed by multiresidue extraction and followed by GC-MS/MS detection. Results Of 28 pesticides investigated, 5 were detected in 90.7 % of the watermelon samples (n = 75) and 3 in 90 % of durian samples (n = 30). Carbofuran, chlorpyrifos, diazinon, dimethoate and metalaxyl were found in watermelons, whereas dichlorvos, dimethoate and metalaxyl were detected in durians. However, their levels were much lower than the recommended MRL values. Conclusions These pesticide levels detected in the fruits are unlikely to harm the consumers; therefore it is safe to eat watermelon and durian in Thailand. While our results found negligible risk associated with pesticide exposure from consuming these common tropical fruits, special precautions should be considered to decrease total exposure to these harmful pesticides from various foods.