A new eddy covariance logging (EClog) system has been developed based on a handheld computer. The logging program, written in C language, reads the digital data from the sonic anemometer and writes it to a CompactFlash card, at the same time showing instantaneous data, means and fluxes on the screen. The program, running under the Linux operating system, proved to be stable and flexible, and consumed little power (0.7 W). These attributes make the system suitable for application in remote areas during long periods of time. The software and installation manuals are made available on the web under free 'public license' agreement. © 2006 Elsevier B.V. All rights reserved.