Cognitive Radios are currently a big challenge for the telecommunications industry. Many efforts are in progress to make communication radio systems as adaptive as possible such that they are aware of their environment and they are self configurable. An ultimate adaptive radio with the specified features is used to be called a Cognitive Radio. A cognitive radio can sense its operating environment's conditions and it is able to reconfigure itself and to communicate with other counterparts based on the status of the environment and also the requirements of the user to meet the optimal communication conditions and to keep quality of service (QoS) as high as possible. In this research a design of a stand-alone (non-centralized) cognitive radio system will be approached. The heart of the cognitive radio is the cognitive engine. The problem of having a cognitive engine to start a non-cooperative communication with other cognitive radios within its range and meeting the QoS requirements imposed by the application, is addressed in this thesis and it is discussed how, by using spectrum holes and adjusting the radio parameters accordingly, this goal is reached. More specifically, a bootstrapping protocol is proposed for the initiation of communication among cognitive radios in the network after which both transmitter and the receiver are configured on the same frequency and tune on the same settings \eg modulation and coding. The other modules discussed in the cognitive radio design are the policy engine, the spectrum sensor and the SDR transceiver. These modules are not part of this research, however, they are included in the design.