The objective of this letter oriented towards microwave measurement of high impedance devices using a conventional on-wafer probe station is multiple. First, we provided a quantification of the measurement uncertainty inherent to the setup when measuring capacitors in the range 0.01-10 fF using both reflection and transmission methods up to 50 GHz. In particular, we demonstrate a clear improvement when using transmission method in series-through configuration. As a practical demonstration, on-wafer MOS voltage-tunable capacitors with capacitances ranging from 0.85 to 1.15 fF are extracted with uncertainties of 130 and 2 aF respectively for both reflection and transmission measurements at 10 GHz. Capacitance fluctuation related to the technological process in the order of 20 aF is then exemplary demonstrated using the series-through configuration. Index Terms-sub-fF MOS varactor, measurement accuracy, on-wafer calibration, vector network analyzer (VNA), two-port measurement, coplanar waveguide (CPW).