Construction of the new Gotthard rail base tunnel through the Central Alps provided a truly unique sample of a fissure assemblage, formed during exhumation and cooling of the Central Alps. The base of the tunnel is at 500m a.s.l. and the overburden at the sampling locality amounts to 2000m. The fissure assemblage apophyllite-(KF), laumontite and quartz occurs within the Southern Aar granite. It formed during exhumation and erosion of the Alpine orogen. Apophyllite and laumontite mark very late fissure minerals in the Central Swiss Alps, only followed by stilbite, hematite, and calcite. The data from a combined study of 40Ar/39Ar age dating of apophyllite, apatite fission-track analysis, and the petrology of rock samples from tunnel and the from the mountains above the tunnel reflect the late stages of an aging orogen. Apatite fission-track analysis yields an exhumation rate of 0.46mm/yr, a cooling rate of 12.3°C/m.y. and a geothermal gradient of 27°C/km at the time of apophyllite formation. Combining these data with the 40Ar/39Ar plateau age of 2Ma for the formation of apophyllite, a minimum formation temperature and depth of 68°C at 2550m below the present day erosion surface follow. At this time, the position of the sample location was 550m below the tunnel level. Assemblage stabilities and computed temperature–time evolution of fissures in the Aar Massif indicate that laumontite formed between 11 and 2Ma ago at temperatures between 180 and ~70°C. Chemical components for forming laumontite were provided from dissolution of minerals of the Alpine greenschist facies Variscan granitoid rocks of the Aar massif basement. Systematic variations in the composition of laumontite are an effect of decreasing temperature. Display omitted ► We present the first effort to date late stage minerals in Alpine fissures. ► Alpine fissures chronology: quartz–laumontite–apophyllite. ► Laumontite is formed at temperatures between 180 and ~70°C. ► Apophyllite age and fission-track data give a minimum formation temperature of 68°C. ► Unique apatite fission-track study of vertical aligned tunnel and surface sample.