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For over three decades much research has been devoted to the identification of founders who could have been the first carriers of different deleterious genes in the French Canadian population. In some cases this research led to an investigation of the European origins of these founders. Using up-to-date data on genealogical records of 673 probands (6 hereditary diseases) and 99 control group individuals bom in the Saguenay region (Quebec, Canada), we show that it is difficult to identify a precise region where a deleterious gene could have originated. By taking several key factors into consideration (founders’ genetic contribution, level of commonness, sex, birth year), we found many possible candidates for each disease, leading to various regions of origin in France (Aunis, Maine, Normandie, Orleanais, Perche, and other provinces) or outside France (British Isles, other European countries). Our results also showed notable differences between the origins of male and female founders. Furthermore, all founders common to at least 95% of the probands of a given disease were also common to 95% of the probands of at least one other disease; among these founders 29 were common to 95% or more of the probands of each group (including the control group).