Particle number size distribution measurements were conducted during the summer of 2012 at City-Centre Urban Background (Patras-C), Urban Background (ICE-HT in Patras, DEM in Athens, EPT in Thessaloniki), and Regional Background stations (FIN in Crete). At the City-Centre Urban Background station, the average number distribution had a geometric mean diameter peak approximately at 60 nm and the highest number concentration, whereas at the Regional Background station and the Urban Background stations it displayed a major peak approximately at 100 nm, with the Regional Background station exhibiting the lowest number concentration. The particle number size distribution at each site was divided into size fractions and, based on their diurnal variation and previous studies, we concluded that the main sources for the City-Centre Urban Background station are traffic and the regional background concentration, for the Urban Background stations fresh traffic, aged traffic, cooking and the regional background concentration, and for the Regional Background station local activities (tourism, cooking) and regional background concentration. The median number concentration that is attributed to regional background concentration for the City-Centre Urban Background, the Urban Background and the Regional Background stations are respectively 13, 29 and 45% of the total number concentration. Nucleation events were identified at DEM station, where the newly formed particles accounted for 4% of the total particle concentration for the measurement period in the size range 10–20 nm, EPT, where they accounted for 12%, and FIN, where they accounted for 1%, respectively. New Particle Formation events contribution during summer to Condensation Cloud Nuclei were therefore insignificant in the Eastern Mediterranean. Modal analysis was performed on the number distributions and the results were classified in clusters. At the City-Centre Urban Background station, the cluster-source that dominated number concentration and frequency is related to fresh and aged traffic emissions, at the Urban Background stations aged traffic emissions, while at the Regional Background station number and frequency were dominated by the regional background concentration. Based on cluster analysis, 18% of the median number distribution was due to long range transport at the City-Centre Urban Background site, 37% at the Urban Background sites, and 59% at the Regional Background site. The Flexible Particle Dispersion Model (FLEXPART) was used in order to acquire geographic origin clusters and we concluded that the Etesian flow increases the median regional background number concentration in the Mediterranean basin by a factor of 2.5–4.