Many theoretical and experimental studies have been carried out in order to study the flow and heat transfer in microchannels. In the recent years, numerical simulation has been applied to investigate the problem under a variety of conditions. However, much of the focus has been on steady-state problems and time-dependent transport has received relatively minor attention, despite its importance in practical electronic devices and systems. Employing a versatile commercial code, this paper aims to examine heat removal from straight rectangular microchannels affected by a time-dependent heat flux input. Both cosinusoidal variation and step-change application and removal of a uniform heat source are studied to determine the response time of the system. For the fluid phase, the two-dimensional momentum and energy equations are solved, considering temperature dependent properties and viscous dissipation. The effects of the amplitude of the heat flux variation, inlet velocity, and geometry, including the thickness of the heat sink, are investigated. Channels of smaller width are found to be more sensitive to the heat flux source, especially for higher input values. The velocity represents the most important parameter for channels of greatest width considered here, as it directly affects the fluid dynamics and the pressure drop when a time-dependent heat source is applied to the system. (C) 2012 Elsevier Ltd. All rights reserved.