As always, the case in Alsace is different. The region has been bandied between Gauls and Germans, and French and Germans since the beginning of time it seems. (See this handy timeline.) It has effected religious practices and the documentation of generations differently from in the rest of France.
In 1529, when it was part of what would become Germany, the senate of Strasbourg, the city of Martin Luther, voted to end Catholicism in the city and that "culte" was banned. Alsace eventually became about 10% Protestant. For all of the 16th century, when Protestants were battling it out against Catholics in France, Alsace was not in France. Part of it was annexed to France in the Treaty of Westphalia of 1648, when Alsatians believed they would not be persecuted, for the Edict of Nantes was still in effect. The rest of the region was annexed in 1674, just a few years before the Edict of Nantes would be revoked. However, imposing absolute adherence to Catholicism was impossible and the existing Protestant traditions and structures continued.
This means that Protestant parish registers were maintained by pastors since the inception of Protestantism and most are preserved in the Archives Départementales. In almost every case, they are in Latin or German, with Gothic script if the latter. The genealogy society of Alsace, the Cercle Généalogique d'Alsace, has transcribed a number of the registers. They have a small data base on their website. They also sell publications containing the transcriptions. Lastly, they have placed some on Généalogie.com, a site one must pay to use.
It also means that one rarely hears the term "Huguenot" in reference to Protestants from Alsace, for they did not generally flee religious persecutions. They fled war.
© 2009 Anne Morddel
The picture above comes from a depressingly jingoistic book for tots, Le Paradis tricolore, by Hansi and pulished in Paris by Fleury in 1918.