Were there any huge differences between Western and Eastern Europe in the medieval era?

How are you defining Eastern Europe and Western Europe?

If you're using the 20th century Cold War era version of Eastern Europe, then that would include places like Poland, Hungary and the Czech lands. These areas were from circa 1000 to the Reformation all closely tied in religion to the Church in Rome, and in this period had increasing waves of settlers from places like Germany and the Netherlands, who established towns and cities governed under various German-originating law codes. The Czech lands (roughly Bohemia and Moravia) were integral parts of the Holy Roman Empire, the King of Bohemia being one of the electors who chose the Emperor. Nowadays in geographic, historic and social science circles these areas are more properly considered parts of Central Europe, rather than Eastern Europe.

Southeastern Europe (roughly the Balkan Peninsula) spent much of this period as part of the Byzantine Empire, or as part of the various Serbian and Bulgar states that came and went in conflict with that empire. They plus most of Hungary were conquered in the 14th-16th centuries by the Ottomans. Further east, in the north there were Baltic and Finnic peoples who were slowly conquered and absorbed by Swedes, Danes, states which would eventually become part of modern Russia, and the Grand Duchy of Lithuania. Further South, the Kievan Rus' broke apart into principalities, which were to various degrees controlled by the Mongols, Tatars and Lithuanians.

Which is all to say that it's probably a mistake to consider "Western Europe" and "Eastern Europe" two discrete halves of a continent, each of which had strong commonalities within it and contrasts with the other. Even in Western Europe during this period. there weren't necessarily greater similarities between Anglo-Saxon or Norman England and the Emirate of Cordoba than between England and, say, Poland or Russian principalities. There were just as many, if not more, differences between North and South and center and periphery than between East and West. Of course I've mostly focused on the later middle ages, and so when one factors that the Medieval Period generally is considered the period to be between 500 and 1500, there are huge differences within the same territory at both ends of that period!