Comprehensive two dimensional GC (GC×GC), coupled to either a time of flight MS (TOF-MS) or a fast scanning quadrupole MS (qMS) has greatly increased the peak capacity and separation space compared to conventional GC-MS. However, commercial GC×GC-TOFMS systems are not equipped with chemical ionization (CI) and do not provide dominant molecular ions or enable single ion monitoring for maximal sensitivity. A GC×GC-qMS in mass scanning mode was investigated with EI and positive CI (PCI), using CH4 and NH3 as reagent gases. Compared to EI, PCI-NH3 produced more abundant molecular ions and high mass structure specific ions for steroid acetates. Chromatography in two dimensions was optimized with a mixture of 12 endogenous and 3 standard acetylated steroids (SM15-AC) relevant to doping control. Eleven endogenous target steroid acetates were identified in normal urine based on their two retention times, and EI and PCI-NH3 mass spectra; nine of these endogenous target steroid acetates were identified in congenital adrenal hyperplasia (CAH) patients. The difference between the urinary steroids profiles of normal individuals and from a CAH patient can easily be visually distinguished by their GC×GC-qMS chromatograms. We focus here on the comparison and interpretation of the various mass spectra of the targeted endogenous steroids. PCI-NH3 mass spectra were most useful for unambiguous molecular weight determination and for establishing the number of -OH by the losses of 1 or more acetate groups. We conclude that PCI-NH3 with GC×GC-qMS provides improved peak capacity and pseudomolecular ions with structural specificity.