I read an article recently that suggested that there was an impact on the Neanderthal populations of Asia and Europe from the diseases introduced by the Homo Sapiens when they first migrated out of Africa, but over time, interbreeding between Homo Sapiens and Homo Neanderthalensis affected immunity and susceptibility to various diseases in each population. Homo Sapiens would have been affected by Neanderthal diseases as well, so it wasn't just a one way gene flow with regard to disease pathogens. The impact of diseases from the different populations likely did not contribute to the extinction of the Neanderthals, as the two populations co-existed in similar spaces for tens of thousands of years before the Neanderthals went extinct. Now, there could have been individual epidemic events that affected small populations, but because Neanderthals lived in smaller groups with more distance between groups, it's unlikely that an epidemic would have spread from group to group in a way that would decimate the population overall. The smaller group size of Neanderthals and the fact that their technology did not advance appreciably in the way that Homo Sapiens technology advanced in the same time period would have disadvantaged the Neanderthals. Interbreeding played a role, but recent genetic studies show that much of the interbreeding occurred early after Homo Sapiens moved into the regions inhabited by Neanderthals, and while there continued to be interbreeding over time, the most active period of interbreeding was closer to the time of first contact. I think it was mainly an issue of difference in technologies, differences in the way society was organized, and the difference in group size that gave Homo Sapiens the definite advantage over Neanderthal groups.

Perhaps but considering that Homo Neanderthalis and Homo Sapiens aren't all that far separated on the evolutionary tree, wouldn't they have had some similar natural immunities to diseases that we also had?
I tend to think that the somewhat 'disappearing' of Neanderthals was more likely a kind of 'natural' progression of the evolutionary processes combined with the inter-breeding of both species and the competition for resources playing their parts more than anything else.
But hey, that's just my thoughts on the matter anyway.

Interesting.