Black carbon (BC) mass, size distribution and mixing state in sub-micron aerosols were characterized from late February to March 2007 using a single particle incandescence method at the high alpine research station Jungfraujoch (JFJ), Switzerland (46.33° N, 7.59° E, 3580 m a.s.l.). JFJ is a ground based location, which is at times exposed to continental free tropospheric air. A median mass absorption coefficient (MAC) of 10.2±3.2 m<sup>2</sup> g<sup>−1</sup> at λ = 630 nm was derived by comparing single particle incandescence measurements of black carbon mass with continuous measurements of absorption coefficient. This value is comparable with other estimates at this location. The aerosols measured at the site were mostly well mixed and aged during transportation via the free troposphere. Pollutant sources were traced by air mass back trajectories, trace gases concentrations and the mass loading of BC. In southeasterly wind directions, mixed or convective weather types provided the potential to vent polluted boundary layer air from the southern Alpine area and industrial northern Italy, delivering enhanced BC mass loading and CN concentrations to the JFJ. The aerosol loadings at this site were also significantly influenced by precipitation, which led to the removal of BC from the atmosphere. Precipitation events were shown to remove about 65% of the BC mass from the free tropospheric background reducing the mean loading from 10±5 ngm<sup>−3</sup> to 4±2 ngm<sup>−3</sup>. Overall, 40±15% of the observed BC particles within the detectable size range were mixed with large amounts of non-refractory materials present as a thick coating around the BC core. The growth of particle size into the accumulation mode was positively linked with the degree of BC mixing, suggesting the important role of condensable materials in increasing particle size as well as enhancing BC mixing state. It is the first time that BC mass, size distribution and mixing state are reported in the free troposphere over Europe. These ground based measurements also provide the first temporal study of BC in the European free troposphere quantitatively measured by single particle methods. At the present time there is only limited information of BC and its mixing state in the free troposphere, especially above Europe. The results reported in this paper provide an important constraint on modelled representation of BC.