We have studied the effects of ion implantation in GaAs using the techniques of deep-level transient spectroscopy. Samples included an unimplanted epitaxial buffer layer, a sample implanted directly into that buffer layer and then capped with Si3N4, a sample implanted into that buffer layer through a similar cap, and a sample implanted directly into a semi-insulating substrate and then capped. All implants were with Si29 and both types of implant were annealed at 860°C for fifteen minutes. We find that the total density of deep levels is not changed significantly by direct implantation, capping and annealing but that implantation through a cap greatly in creases the total deep-level concentration. Deep levels found in implanted layers after capping and annealing are primarily characteristic of the substrate or buffer layer into which the implantation is made, unless the implant is through a cap in which case contaminants from the capping process may be evident at high densities.