An incoherent scatter experiment using alternating coded pulses has been implemented at Jicamarca. The experiment is intended to facilitate aeronomy research in the topside and protonosphere. By virtue of utilizing the full duty cycle capabilities of the radar transmitter, the experiment has improved sensitivity over the conventional double pulse experiment and permits multiple parameter estimation at protonospheric altitudes. Error analysis, including the estimation of the complete error covariance matrix for the alternating coded pulses, is discussed. Example density, temperature, and composition data illustrate the capabilities of the new experiment. ¿ 2000 American Geophysical Union