Nowadays, mobile communications are characterized by a fast-increasing demand for internet-based services (voice, video data). Video services constitutes a large fraction of the internet traffic today. According to a report by Cisco, 75% of the world's mobile data traffic will be video-based by 2020. This ever-increasing demand in delivering internet-based services, has been the main driver for the development of the 4G digital cellular network, where packet- switched services are the primary design target. In particular, the overall system needs to ensure high peak data rates to the user and low delay in the delivery of the content, in order to support real time applications such as video streaming and gaming. This has motivated, in the last decade, a renewed and raising interest and research in wireless radio access technology. Wireless channel suffers from various physical phenomena like path-loss, shadowing, fading, interference, etc. In the most recent technologies, these effects are contrasted using Automatic Repeat re-Quest (ARQ) protocol, which consist on the retransmission of the same signal from the same node. ARQ protocol is usually combined with channel codes at the physical layer, which is known as Hybrid Automatic Repeat re-Quest (HARQ) protocol. Another improvement for communications over wireless channels is achieved when Relays are used as intermediate nodes for helping the communication between a Source and a Destination, which is known as cooperative communication. Both techniques, cooperation and HARQ, if individually applied, significantly improve the performance of the communication system. One open question is whether their combination would bring the sum of the singular improvements, or be only marginally beneficial. In the literature we can find many studies for the combination of these two techniques, but in our thesis we focus mainly on this interaction at the level of the physical layer (PHY) and the medium access control layer (MAC). We use example protocols on a network of three nodes (Source, Destination and Relay). For the theoretical analysis of these systems we focus on Finite State Markov Chains (FSMC). We discuss the case where Relay works in Decode-and-Forward (DCF) mode, which is very common in the literature, but our analysis focuses more strongly on the case where the Relay works in Demodulate-and-Forward (DMF) mode, because of its simplicity of implementation and its efficiency. This case is much more rarely addressed in the available literature, because of the higher complexity required by its analysis. Usually, the interaction between the two techniques has been studied using deterministic protocols, but in our analysis we will focus on both, deterministic and probabilistic protocols. So far, probabilistic protocols, where the retransmitting node is chosen with a given probability, have been mainly proposed for higher layers of communication systems, but, in contrast, this thesis studies probabilistic protocols on the physical layer and MAC layer, which give more insight on the analysis and performance optimization. The probabilistic protocols contains very few parameters (only 2) that can be optimized for best performance. Note that these parameters can be computed to mimic the behavior of a given deterministic protocol, and the result of the probabilistic protocol after optimization can only improve over this one. Moreover, the performance of our optimized probabilistic protocol is checked against results of the literature, and the comparison shows that our protocol performs better. In the end, there is also discussed the issue of relay selection. In a scenario of several candidate Relays, we propose a criterion for choosing the best Relay. The performance obtained by this criterion is compared to that obtained with the reference criteria in the literature.