Solid phase microextraction (SPME) was evaluated for use in the quantification of aroma volatile production by Granny Smith apples during cool storage. Particular attention was paid to quantifying alpha-farnesene (3,7,11-trimethyldodeca-1,3(E),6(E),10-tetraene) due to its involvement in superficial scald, a disorder of cool stored apples. Comparison between SPME and solid phase extraction (SPE) showed that the SPME fiber had greater adsorption of high molecular weight (MW) volatiles such as alpha-farnesene. When sampling by SPME, these higher MW volatiles did not equilibrate between apples, headspace, and fiber within sampling times as long as 90 min, while lower MW volatiles equilibrated within 5 min. This behavior was also shown by a simple model system consisting of five selected volatiles dissolved in an involatile, lipophilic liquid (squalane). The less volatile high MW aroma compounds evaporated slowly from the surface of the apples and were depleted from the headspace because of very rapid adsorption by the SPME fiber. The amount of alpha-farnesene adsorbed by the fiber increased with air movement through the system. In a static headspace system, the amount of alpha-farnesene adsorbed by the fiber decreased nonlinearly with increasing distance from the apples, due to adsorption onto the glass walls. While SPME is ideal for rapid, qualitative determination of apple headspace volatiles, the slower equilibration of higher MW volatiles limits its use for quantification in more complex systems.