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The safety of vegetable oils has come under intense scrutiny ever since the International Agency for Research on Cancer issued an alert on the carcinogenic properties of 3-monochloropropane-1,2-diol fatty acid esters (3-MCPDE) and glycidyl esters (GE). In this study, a total of 114 samples of artisanal palm oil (PO), palm kernel oil (PKO), and coconut oil (CO) were sourced from three regions in Ghana. The concentrations of 3-MCPDE and GE were quantified using the indirect method with gas chromatography-mass spectrometry. Subsequently, the statistical distribution functions of the concentrations of the esters were fitted using the Palisade @risk software. The relationships between the esters in the oils were determined using the Pearson correlation coefficient. The results showed no correlation (p > 0.05) between the concentrations of 3-MCPDE and GE. However, 18–60 % of the sampled PO contained 3-MCPDE above the European Commission's 2.5 mg/kg limit. In comparison, 24–35 % of the PO contained GE at levels exceeding the Commission's 1 mg/kg limit. Similarly, 25–35 % of PKO samples had GE concentrations above the limit. CO was the least contaminated oil, with little or no evidence of 3-MCPE and GE formation. Though the most frequently occurring (modal) concentrations of the esters were below the limits imposed by the Commission, it is the 95th percentile level of concentrations, especially for PO, that pose a health concern. Serious education and control must be exercised over the production of PO to enhance safety at the national and international markets.