Accurate and precisely located self-potential (SP), temperature (T) and CO2 measurements were carried out in the summit area of Stromboli along 72 straight profiles. SP data were acquired every metre and T data every 2.5 m. CO2 concentrations were acquired with the same density as T, but only along seven profiles. The high density of data and the diversity of the measured parameters allows us to study structures and phenomena at a scale rarely investigated. The shallow summit hydrothermal activity (Pizzo-Fossa area) is indicated by large positive SP, T and CO2 anomalies. These anomalies are focused on crater faults, suggesting that the fracture zones are more permeable than surrounding rocks at Stromboli. The analysis of the distribution of these linear anomalies, coupled with the examination of the geologic, photographic and topographic data, has led us to propose a new structural interpretation of the summit of Stromboli. This newly defined structural framework comprises (1) a large Pizzo circular crater, about 350 m in diameter; (2) a complex of two concealed craters nested within the Pizzo crater (the Large and the Small Fossa craters), thought to have formed during the eruption of the Pizzo pyroclastites unit; the Small Fossa crater is filled with highly impermeable material that totally impedes the upward flow of hydrothermal fluids; and (3) The present complex of active craters. On the floor of the Fossa, short wavelength SP lows are organized in drainage-like networks diverging from the main thermal anomalies and converging toward the topographic low in the Fossa area, inside the Small Fossa crater. They are interpreted as the subsurface downhill flow of water condensed above the thermal anomalies. We suspect that water accumulates below the Small Fossa crater as a perched water body, representing a high threat of strong phreatic and phreatomagmatic paroxysms. T and CO2 anomalies are highly correlated. The two types of anomalies have very similar shapes, but the sensitivity of CO2 measurements seems higher for lowest hydrothermal flux. Above T anomalies, a pronounced high frequency SP signal is observed. Isotopic analyses of the fluids show similar compositions between the gases rising through the faults of the Pizzo and Large Fossa craters. This suggests a common origin for gases emerging along different structural paths within the summit of Stromboli. A site was found along the Large Fossa crater fault where high gas flux and low air contamination made gas monitoring possible near the active vents using the alkaline bottle sampling technique.