The region encompassing Santa María, Cerro Quemado, and Zunil volcanoes, close to Quetzaltenango, the second largest city of Guatemala, is volcanically and tectonically complex. In addition, the huge Xela caldera, about 20km in diameter, crosses this area and links up to the important Zunil fault zone located between the three volcanoes. Two highly active geothermal sites, named Zunil-I and Zunil-II, are also located between these three volcanic edifices at the southeastern boundary of Xela caldera. In order to determine the permeability variations and the main structural discontinuities within this complex volcano-tectonic setting, self-potential and soil CO2 flux measurements have been coupled, with a step of 20m, along a 16.880km-long profile crossing the entire area. Two shallow hydrothermal systems, with maximum lateral extensions of 1.5km in diameter, are indicated by positive self-potential/elevation gradients below Santa María and Cerro Quemado volcanoes. Such small hydrothermal systems cannot explain the intense geothermal manifestations at Zunil-I and Zunil-II. Another minor hydrothermal system is indicated by self-potential measurements on the flank of Santa María along the edge of the Xela caldera. CO2 flux measurements display slight variations inside the caldera and decreasing values crossing outside the caldera boundary. We hypothesize the presence of a magmatic body, inside the southeastern border of Xela caldera, to explain the deeper and more intense hydrothermal system manifested by the Zunil-I and the Zunil-II geothermal fields. This magmatic system may be independent from Santa María and Cerro Quemado volcanoes. Alternatively, the hypothesized Xela magmatic system could have a common magmatic origin with the Cerro Quemado dome complex, consistent with previous findings on regional gas emissions. Sectors bordering the Cerro Quemado dome complex also have high amplitude minima-short wavelength anomalies in self-potential, interpreted as preferential rain water infiltration along faults of major permeability, probably related with the most recent stages of Cerro Quemado dome growth. © 2010.