Morpholine salts of fatty acids have been used in wax coatings on the surfaces of fruit and vegetable commodities in China and the United States, etc. However, morpholine usage was prohibited in many other countries because of safety concerns. We optimized analytical methods to determine morpholine in the peel and pulp of fruits and vegetables by gas chromatography-mass spectrometry (GC-MS). This morpholine analysis method was applied to real samples of apples, citrus fruits, and vegetables from Korea, China, and the U.S. The method was validated using apple and citrus fruit peels and pulp. The method detection limit (MDL) was 1.3–3.3 µg/kg. The recovery rates of morpholine were 88.6–107.2% over a fortified level of 10–400 µg/kg. Intra-day and inter-day precisions were 1.4–9.4% and 1.5–2.8%, respectively. The morpholine concentrations were n.d. (not detected)–11.19 and n.d. (not detected)–12.82 µg/kg in apple and citrus peels, respectively. Morpholine was not detected in citrus or apple pulp samples or in vegetable samples.