It is generally recognized that the traffic generated by an individual connected to a network acts as his biometric signature. Several tools exploit this fact to fingerprint and monitor users. Often, though, these tools assume to access the entire traffic, including IP addresses and payloads. This is not feasible on the grounds that both performance and privacy would be negatively affected. In reality, most ISPs convert user traffic into NetFlow records for a concise representation that does not include, for instance, any payloads. More importantly, large and distributed networks are usually NAT'd, thus a few IP addresses may be associated to thousands of users. We devised a new fingerprinting framework that overcomes these hurdles. Our system is able to analyze a huge amount of network traffic represented as NetFlows, with the intent to track people. It does so by accurately inferring when users are connected to the network and which IP addresses they are using, even though thousands of users are hidden behind NAT. Our prototype implementation was deployed and tested within an existing large metropolitan WiFi network serving about 200,000 users, with an average load of more than 1,000 users simultaneously connected behind 2 NAT'd IP addresses only. Our solution turned out to be very effective, with an accuracy greater than 90%. We also devised new tools and refined existing ones that may be applied to other contexts related to NetFlow analysis.