Canada's forests play an important role in the global carbon cycle through carbon (C) storage and C exchange with the atmosphere. While estimates of aboveground biomass have been improving, little is known about belowground C storage in root biomass. Here we estimated the contribution of roots to the C budget of Canada's 2.3 × 106 km2 managed forests from 1990 to 2008 using the empirical modeling approach of the Carbon Budget Model of the Canadian Forest Sector (CBM-CFS3) driven by detailed forestry data sets from the National Forest C Monitoring, Accounting and Reporting System. The estimated average net primary production (NPP) during this period was 809 Tg C yr−1 (352 g C m2 yr−1) with root growth and replacement of turnover contributing 39.8 % of NPP. Average heterotrophic respiration (Rh) was 738 Tg C yr−1 (321 g C m−2 yr−1), which resulted in a net ecosystem production (NEP) value of 31 g C m−2 yr−1(71 Tg C yr−1), and on average only 8.7% of NPP remained in the system as NEP. Estimated average root C stocks were 2.38 Pg (1235 g C m−2), mostly in coarse roots (≥ 5 mm diameter), and had an average root to shoot percentage (belowground to aboveground biomass) of 25.6%. Detailed monitoring of C exchange between forests and the atmosphere and an improved understanding of the belowground processes and their response to environmental changes are needed to improve our understanding of the terrestrial C budget.