Auroral processes are evident in Jupiter's polar atmosphere over a large range in wavelength (X-ray to radio). In particular, previous observations in the mid-infrared (5 to 15 µm) have shown enhanced emission from CH 4 , C 2 H 2 and C 2 H 4 and further stratospheric hydrocarbon species in spatial regions coincident with auroral processes observed at other wavelengths. These regions, described as auroral-related hotspots, observed at approximately 160• W to 200• W (System III) at high-northern latitudes and 330• W to 80• W at high-southern latitudes, indicate that auroral processes modify the thermal structure and composition of the neutral atmosphere. However, previous studies have struggled to differentiate whether the aforementioned enhanced emission is a result of either temperature changes and/or changes in the concentration of the emitting species. We attempt to address this degeneracy in this work by performing a retrieval analysis of Voyager 1-IRIS spectra (acquired in 1979) and Cassini-CIRS spectra (acquired in 2000/2001) of Jupiter. Retrievals of the vertical temperature profile in Cassini-CIRS spectra covering the auroral-related hotspots indicate the presence of two discrete vertical regions of heating at the 1-mbar level and at pressures of 10-µbar and lower. For example, in Cassini-CIRS 2.5 cm −1 'MIRMAP' spectra at 70• N (planetographic) 180• W (centred on the auroral oval), we find temperatures at the 1-mbar level and 10-µbar levels are enhanced by 15.3 ± 5.2 K and 29.6 ± 15.0 K respectively, in comparison to results at 70• N, 60• W in the same dataset. High temperatures at 10-µbar and lower pressures were considered indicative of joule heating, ion and/or electron precipitation, ion-drag and energy released form exothermic ion-chemistry. However, we conclude that the heating at the 1-mbar level is the result of either a layer of aurorally-produced haze particles, which are heated by incident sunlight and/or adiabatic heating by downwelling within the auroral hot-spot region. The former mechanism would be consistent with the vertical profiles of polycyclic aromatic hydrocarbons (PAHs) and haze particles predicted in auroral-chemistry models (Wong et al., 2000(Wong et al., , 2003. Retrievals of C 2 H 2 and C 2 H 6 were also performed and indicate C 2 H 2 is enriched but C 2 H 6 is depleted in auroral regions relative to quiescent regions. For example, using CIRS ∆ν = 2.5 cm −1 spectra, we determined that C 2 H 2 at 0.98 mbar increases by 175.3 ± 89.3 ppbv while C 2 H 6 at 4.7 mbar decreases by 0.86 ± 0.59 ppmv in comparing results at 70• N, 180• W and 70• N, 60• W. These results represent a mean of values retrieved from different initial assumptions and thus we believe they are robust. We believe these contrasts in C 2 H 2 and C 2 H 6 between auroral and quiescent regions can be explained by a coupling of auroral-driven chemistry and horizontal advection. Ion-neutral and electron recombination chemistry in the auroral region enriches all C 2 hydrocarbons but in particular, the unsaturated ...