This is a really good question and one that's been argued for years. The current view is that German anti-Semitism was rather insignificant prior to the rise of Nazism. The Nazis, on the current view, lent Anti-Semitism a degree of intellectual respectability, see Fritzsche's Germans into Nazis.

Against this view is the idea that German history, especially anti-Semitism, can be traced from, as William L. Shirer put it, "Luther to Hitler." See Shirer's The Rise and Fall of the Third Reich, which, while not an academic history, provides one of the best known expositions of the idea.

I have to leave now, but when I get back, I'll explain along the lines of the Sonderweg and against the Sonderweg. The Sonderweg holds that, due to an incomplete modernization, German society maintained "pre-modern" attitudes, such as anti-Semitism, militarism, etc. The argument here is that the Nazis mobilized existing anti-Semitic attitudes and then exacerbated them. However, as Blackbourn and Eley pointed out in their book The Peculiarities of German History, that's only half an answer. The model of modernization used is one that treats the US and UK as normative, rather than exceptional. Blackbourn and Eley instead argue that there is no normative path of modernization, and you can't talk about German peculiarities, but particularities.

So to answer your question, at least in a long-winded way, I would argue that you can't really draw a straight line from the German Empire to anti-Semitism under the Nazis. I'm sympathetic to the Sonderweg in a lot of areas, especially in explaining World War I, but I don't see the evidence there. Actually, prior to World War I, Germany was probably among the less anti-Semitic countries.