Cyclopiazonic acid (CPA) is an important mycotoxin given its toxicity and prevalence in foods and feeds. There is tremendous interest in developing analytical methods that include CPA as part of a multi-residue mycotoxin routine, but there appears to be considerable difficulty in analysing it using liquid chromatography with electrospray ionisation tandem mass spectrometry (LC-MS/MS). During the development of a multi-residue method for mycotoxins including CPA, a number of issues were discovered under routine and common analytical conditions that have an impact on the determination of CPA, including: (1) at the ng/ml level CPA reacts with ambient oxygen from the headspace of the vial, an effect that decreases its concentration linearly; (2) CPA readily adsorbs to plastic in a reversible fashion; (3) CPA is acid hydrolysed with formic acid; (4) CPA reacts with the column stationary phase affecting chromatographic parameters; and (5) CPA presents significant carry-over issues. In an effort to find solutions to these problems we found that CPA can be protected from reacting with oxygen by adding 1 µg/ml ascorbic acid and that its carry-over can be reduced to a negligible level by injecting ammonia between injections of solutions containing CPA, even with formic acid in the mobile phase. Chromatographic conditions for CPA have been optimised in consideration of all of the aforementioned concerns.