In Medieval times, creating musical manuscripts was quite expensive (due to the cost of parchment, and the time needed for a scribe to copy it down), so only wealthy establishments were able to create them. This mostly included churches and monasteries. At that time, the Church was the focal point of social life, learning and the arts. Today, unfortunately, we can only study the small amount of music that was written and has survived.
At the beginning of the medieval era, the notated music is assumed to be monophonic and homorhythmic with what appears to be a unison sung text. This music also had no notated instrumental accompaniment. Actual rhythms didn't appear in music manuscripts until the 12th or 13th centuries; however the rhythmic complexity that was realized in this music is comparable to that in the 20th century. During this time, composers were not all that concerned with how their written music was performed. They gave little notice to what instrument (or instruments) would play a piece and never indicated particular instruments within their scores.
Instruments used to perform medieval music still exist, though in different forms. The flute was once made of wood rather than silver or other metal, and could be made as a side-blown or end-blown instrument. The recorder, on the other hand, has more or less retained its past form.