A deep objective-prism survey for H-alpha emission stars towards the Canis Major star-forming clouds was performed. A total of 398 Halpha emitters were detected, 353 of which are new detections. There is a strong concentration of these H-alpha emitters towards the molecular clouds surrounding the CMa OB1 association, and it is likely that these stars are young stellar objects recently born in the clouds. An additional population of H-alpha emitters is scattered all across the region, and probably includes unrelated foreground dMe stars and background Be stars. About 90% of the H-alpha emitters are detected by WISE, of which 75% was detected with usable photometry. When plotted in a WISE colour-colour diagram it appears that the majority are Class II YSOs. Coordinates and finding charts are provided for all the new stars, and coordinates for all the detections. We searched the Gaia-DR2 catalogue and from 334 Halpha emission stars with useful parallaxes, we selected a subset of 98 stars that have parallax errors of less than 20% and nominal distances in the interval 1050 to 1350pc that surrounds a strong peak at 1185pc in the distance distribution. Similarly, Gaia distances were obtained for 51 OB-stars located towards Canis Major and selected with the same parallax errors as the H-alpha stars. We find a median distance for the OB stars of 1182pc, in excellent correspondence with the distance from the H-alpha stars. Two known runaway stars are confirmed as members of the association. Finally, two new Herbig-Haro objects are identified.