The Neolithic decline was a rapid collapse in populations between five and six thousand years ago (approximately 3000 BC) during the Neolithic period in western Eurasia. The specific causes of that broad population decline are still debated.

Source : Wikipedia

There are several theories proposed to explain the global rapid decline. One prominent idea is that agricultural conditions became more difficult due to climate changes. Another is that some kind of fatal viral or bacterial disease became endemic (evidence of plague bacteria,Yersinia pestis, have been found in Neolithic grave sites).

Further reading :

European Neolithic societies showed early warning signals of population collapse

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline