The official language of the present Czech Republic is Czech. All the official documents are written in this language since the founding of the republic in 1918 (with pause of the WWII when the country belonged to Germany). The situation was quite different in the past.
Bohemia, Moravia and Silesia belonged to the Hapsburg dynasty and Austrian empire between 1526 and 1918. The official language of Hapsburgs was German, so it was expected that all officials will be able to speak, read and write in this language. However the official language of the church was Latin, therefor the church documents were mostly written in this language.
Czech language was used in the oldest registries (parish books), because the records there were written not only by the priest, but also by the municipal scribe, teacher or anyone else who was able to write. This was changed in the first third of 18th century when it was ordered by the church that only a priest have to write into registries.
Since then the registries were held in Latin. Some records are very short, other are long and in rich language - it depended on the priest. This was again changed at the end of 18th century, during the reign of Emperor Josef II. He issued an act that said the registries were official document of the empire. The language allowed in the registries was German, but also Czech was used. It again depended on the person who was administering the registries.
German and Czech was then used until the end of Austrian Empire in 1918. There are area where records in one registry were both in Czech and German, because some families were of Czech nationality and others of German. This can be found mainly in large towns and Sudeten area.