In the ionosphere the electromagnetic wave has to pass through the ionized medium which decreases the group velocity of the radio pulses, making the propagation speed less than the free-space speed of light c. This makes the VH h′ greater than the true height h. A certain procedure, known as true height analysis, needs to be applied in order to recreate the true height electron density profile N e (h) from the VH data.Two of the most commonly used true height inversion algorithms are POLynomial ANalysis (POLAN) (Titheridge, 1988) and NhPC (Reinisch et al., 2005;Reinisch & Xueqin, 1983), with the latter being a component of the Automatic Real-Time Ionogram Scaler with True height (ARTIST) software that is widely used in the ionospheric research community. Both algorithms determine the true height using polynomial analysis. POLAN expresses each ionospheric layer in terms of sixth-order overlapping polynomials, whereas the NhPC algorithm describes the layers in terms of shifted Chebyshev polynomials. Both algorithms model the transition in the valley region between E and F layers. Additionally, some ionosonde operators employ the Autoscala algorithm (Pezzopane et al., 2010) which is based on image recognition and parametrization of empirical curves. This paper describes a new method for the electron density profile retrieval from VH measurements using data assimilation. Data assimilation methods incorporate observations into models, providing a description of the system that is optimally consistent with both the model and data. The components that are necessary to build a data assimilation model include a background model, the observations, the observation operator that maps the observations to the model state, and an optimization method that gives an optimal analysis by incorporating the observations into the model. Numerous ionospheric data assimilation methods Abstract A new method is developed to retrieve electron density profiles from a raw virtual height ionosonde traces. A Kalman filter is used for the assimilative inversion scheme together with the newly developed data-driven vertical covariance model. The detailed mathematical formalism for the derivation of the Jacobian that takes into account the effect of the magnetic field is presented. The incoherent scatter radar measurements from Arecibo observatory are employed as the known truth to simulate the virtual height data. The results show that the data assimilative inversion technique accurately retrieves the vertical structure of the ionospheric density at the bottom side of the profile and reconstructs the vertical and temporal small-scale density variations. A comparison with the results obtained by the POLynomial ANalysis (POLAN) inversion algorithm is presented. The assimilative inversion systematically outperforms the accuracy of the POLAN algorithm, on average reducing the percent errors in the electron density by half. Additionally, the simultaneous data ingestion is compared to the sequential assimilation of the virtual height data. FORSYTHE ET AL.