The National Aeronautics and Space Administration Micropulse Lidar Network Version 3 cloud detection algorithm is described and its differences relative to the previous version highlighted. Clouds are identified from normalized Level 1 signal profiles using two complementary methods. The first considers signal derivatives vertically for resolving low-level clouds. The second, which resolves high-level clouds like cirrus, is based on signal uncertainties given the relatively low signal-to-noise ratio exhibited in the upper troposphere by eye-safe network instruments, especially during daytime. Furthermore, a multi-temporal averaging scheme is used to improve cloud detection under conditions of weak signal-to-noise. Diurnal and seasonal cycles of cloud occurrence frequency based on one year of measurements at the Goddard Space Flight Center (Greenbelt, MD) site are compared for the new and previous versions. The largest differences, and perceived improvement, in detection occurs for high clouds (above 5-km, mean sea level) which increase in occurrence by nearly 6%. There is also an increase in the detection of multi-layered cloud profiles from 9% to 20%. Macrophysical properties and estimates of cloud optical depth are presented for a transparent cirrus dataset. However, the limit to which molecular signal can be reliably retrieved above cirrus clouds occurs between cloud optical depths of 0.5 and 0.8.