Are There Hidden Toxins in Your Average Cup of Coffee?

Heather L McGhee, Julie L Brunkhorst, Jenny B Rodgers, Brendan McGhee and Ronald Niemeijer

Trilogy Analytical Laboratory, Washington, MO 63090




Coffee is one of the most consumed beverages in the United States and worldwide. It is also one of the largest exports of developing countries. The average American drinks 3.1 cups of coffee per day and the United States purchases over $40 billion dollars of coffee each year. The manner in which coffee is harvested, processed and stored is a critical factor for the quality of the coffee. Moldy coffee beans have the potential to generate coffee contaminated with mycotoxins, which can produce major health risks to consumers.

An LC-MS/MS method was used to determine the mycotoxin content of various coffee beans. Green coffee beans were purchased and evaluated for several mycotoxins, specifically Ochratoxin A, Aflatoxins, Sterigmatocystin, Fumonisins, Beauvericin and Enniatins. The green coffee beans were also roasted to various levels to determine if mycotoxin content was affected.  Samples were also purchased “off the shelf” and evaluated for mycotoxin content.


Green coffee samples were obtained and roasted to light, medium and dark roasts using an air-pop popcorn machine.  These samples, as well as 30 samples purchased from various stores and 5 green coffee extract samples, were tested for mycotoxins.

Aflatoxins, Sterigmatocystin, Beauvericin and Enniatins

  • Extraction: 84/16 Acetonitrile/Water solution, shaken for an hour then filtered through a coffee filter.
  • Cleanup: Trilogy M160 cleanup column

Fumonisins, Ochratoxin

  • Extraction: 3/1 Methanol/Water solution, shaken for an hour then filtered through a coffee filter.
  • Cleanup: Trilogy MT3000 column.

All samples were analyzed on an AB Sciex 5500 Q-Trap and 6500+ Q-Trap

Coffee Beans



Coffee Chart 1

Coffee Chart 2

Coffee Chart 3

Coffee Graph



All Samples analyzed were negative for Aflatoxin-B1,B2,G1,G2, Deoxynivalenol, Fumonisin- B1, B2, B3, Enniatin -A, A1, B, B1, HT2 Toxin, T2 Toxin and Zearalenone.

Beauvericin, Ochratoxin A and Sterigmatocystin were most commonly found in the coffee samples, though at low levels.

Minimal Ochratoxin A was found in low levels (below 1 ppb) in some of the green coffee samples. Several “off the shelf” samples had low levels of Ochratoxin and surprisingly, several of the green coffee extract samples contained low levels of Ochratoxin (4–5ppb). 

All of the six  “off the shelf” coffee samples that advertised “certified organic coffee beans” contained at least one mycotoxin. Samples contaminated with Ochratoxin, Sterigmatocysin and Beauvericin are the same brand and certified organic beans.

Since the green coffee samples were divided into 4 equal parts and then roasted, the homogeneity of samples was compromised. Because of this, some mycotoxins appear in one roast level and not other roasts of the same sample . Some samples did have mycotoxin contamination in all roasts and there was no perceived decease in the contamination with the darker roasts.



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