This study examined pesticide residue levels in three fresh fruit varieties commonly consumed in Lagos state, Nigeria. The fruits (apple, watermelon and sweet orange) were collected from various sale points of fruits in three local government areas; Eti-osa (Ajah), Lagos mainland (Oyingbo) and Ifako-ijaiye (Ifako-Ijaiye). Pesticide residue levels were determined using gas chromatography/mass spectrometry (GC-MS). Data obtained from GC-MS were statistically analysed using graph pad prism 6.0 software and compared with WHO/FAO limits. There was no significant difference (P> 0.05) in each fruits obtained per sampling location. Fruits contained pesticides below WHO/FAO limit except for watermelon that had mean pesticide residue concentration for atrazine (0.088-0.133 mg/kg), clothianidin (0.00 - 0.029 mg/kg), omethoate (0.094 - 0.205 mg/kg) and oxamyloxime (0.088 - 0.125 mg/kg) above WHO/FAO MRLs of 0.02, 0.02, 0.01 and 0.03 mg/kg for atrazine, clothianidin, omethoate and oxamyloxime respectively. The presence of pesticides in these fruits calls for strict regulation of the application of pesticides in farms and preservation chambers. This study recommends further investigation of all agricultural produce in order to circumvent contamination and other problems associated with pesticide accumulation and toxicity.