Recently, much attention has been paid to the green design of wireless communication systems using energy efficiency (EE) metrics that should capture all energy consumption sources to deliver the required data. In this paper, we design an energyefficient relay assisted communication system based on estimated channel state information (CSI). It employs amplify-andforward relaying and switches between different communication schemes, which are known as direct-transmission, two-hop and cooperative-transmission schemes, using the estimated CSI in order to maximize the EE. Two estimation strategies are assumed, namely disintegrated channel estimation and cascaded channel estimation. To formulate an accurate EE metric for the proposed opportunistic amplify-and-forward system, the channel estimation cost is reflected on the EE metric by including its impact in the signal-to-noise ratio term and in the energy consumption during the channels estimation phase. Based on the formulated EE metric, we propose an adaptive power allocation algorithm to maximize the EE of the proposed opportunistic amplify-andforward system with channel estimation. Furthermore, we study the impact of the estimation parameters on the proposed system via simulation examples.