Measurements of the energy spectra of secondary particles produced by galactic cosmic rays and trapped protons due to the nuclear interactions of these particles with the Shuttle shielding provide a powerful tool for validating radiation transport codes. A code validated in this way can be used to better estimate the dose and dose equivalent to body organs, measurements that cannot be made directly. The principal cause of single event upsets in electronic devices in the region of the South Atlantic Anomaly is secondary particles, and even in the region of galactic cosmic radiation a significant fraction is produced by secondary particles. In this paper, we describe the first direct measurements of the energy spectra of secondary protons, deuterons, tritons, 3He and 4He produced by galactic cosmic rays inside the Space Shuttle using a charged particle spectrometer. A comparison of these spectra with radiation transport code HZETRN showed reasonably good agreement for secondary protons. However, the code seriously underestimated the flux of all other light ions. The code has been modified to include pick-up and knock-on processes. The modified code leads to good agreement for deuterons and 3He but not for other light ions. This revised code leads to about 10% higher dose equivalent than the original code under moderate shielding, if we assume that higher charge ion fluxes are correctly predicted by the model.