A method, system and computer readable medium for tracking changes in average glycemia in diabetes is based on a conceptually new approach to the retrieval of SMBG data. Using the understanding of HbA1c fluctuation as the measurable effect of the action of an underlying dynamical system, SMBG provides occasional glimpses at the state of this system and, using these measurements, the hidden underlying system trajectory can be reconstructed for individual diabetes patients. Using compartmental modeling a new two-step algorithm is provided that includes: (i) real-time estimate of HbA1c from fasting glucose readings, updated with any new incoming fasting SMBG data point(s), and (ii) initialization and calibration of the estimated HbA1c trace with daily SMBG profiles obtained periodically. The estimation of these profiles includes a factorial model capturing daily BG variability within two latent factors.