Voyager ultraviolet spectrometer (UVS) measurements provided the first unassailable evidence for particle precipitation in the Jovian atmosphere. Strong Lyman and Werner band emissions at high latitudes indicate particle precipitation energy fluxes of about 10 ergs cm-2 s-1. On the other hand dayglow Lyman and Werner emissions at mid- and low-latitudes may indicate additional particle precipitation fluxes on the order of 0.3 ergs cm-2 s-1 at all latitudes. Such particle precipitation can have signficant aernomical effects on the Jovian thermosphere and ionosphere. A one-dimensional theoretical model is used to study these effects for the case of electron precipitation, although ion precipitation produces similar effects. Diffusion equations are solved for all the major neutral species and for H+, and photochemical solutions are given for short lived ions. These and ionospheric components of the model are coupled with the electron and ion energy equations and a two-stream electron transport code that calculates the energy depostion of precipitating electrons (considered to be the precipitating particles) and photoelectrons. An independent calculation of the vertical neutral temperature is also obtained. The results of the model calculations can be broadly categorized as effects of electron precipitation (1) on the neutral composition and temperature of the thermosphere, and (2) on the composition and structure of the ionosphere. Auroral electron precipitation by 10-keV electrons with a total energy flux of 10 ergs cm-2 s-1 produces 4.7¿1011 H atoms cm-2 s-1 and 5 ergs cm-2 s-1 of heat, over 2 orders of magnitude larger than solar EUV processes that produce 3.3¿109 H atoms cm-2 s-1 and 0.03 ergs cm-2 s-1 of heat. Thus, Jovian auroral H production coupled with aurorally driven meridional winds in the thermosphere can possibly explain the high concentration of atomic hydrogen in the low-latitude Jovian upper atmosphere. Furthermore, aurorally produced changes in composition can create important feedback which affects the relative airglow efficiencies and heating rates in the high-latitude thermosphere. In addition, ionization and vibrational heating of H2 from precipitation processes appear to play a central role in determining the structure of the high-latitude ionsphere. Theoretical fits to the Voyager radio occultation electron density profiles at high latitudes suggest a 10-keV electron aurora with an energy flux of 10 ergs cm-2 s-1 coupled with a height-dependent H2 vibrational temperature that reaches 3000 K in the topside ionosphere.