Abstarct: With the development of science and technology in recent years, a new branch of communication name molecular communication is proposed in electrical conferences. Molecular communication is not a simple development traditional network, but this type of communication is a sample completely new communication, which many communication processes are designed to imitate biological systems found in nature. Molecular communication networks are collection of nano-machines connected that through publish and share information new applications that by current technology is not possible proposed. Among the several methods of communication between the nano-machines that have been proposed, using a moleculs reason of very high proportion with dimensions and the environment is the best possible option. Communication molecule is a new interdisciplinary field of information and communication technology, biotechnology and nanotechnology, that data are sent and received through the molecules. Due to the many difference of traditional communication and molecular communication, many aspects of communication such as routing, coding, send and receive data, issues related to noise and security have not been studied properly in this type of communication and there is still a lot of work remains. In a molecular communications, transmitter coded information at molecules concentrations similar to amplitude modulation in classic communication, this means that for send one, transmitter release concentration includes M molecule in environment and not send anything for write zero. Molecules distributed in the environment influenced by factors such as noise, interference and flow are to make to the receiver, and the receiver baxsed on threshold is decided the transmitter has sent zero or one. This means that if the number of molecules reached on receiver more than the threshold, receiver decides that the transmitter has one Send, and if the number of molecules is less than the threshold value transmitter sent the zero. In this thesis, in addition to introducing a molecular communication system which consists of transmitter, channel and receiver, tried to discussion about parameters of the molecular communication such as noise, interference, changing the distance beetwen receiver and transmitter, flow and number of molecules sent by the transmitter that affect system performance. For this purpose we first obtained the probability of error relation to on these parameters and the effect of each of these parameters have investigated on probability of error. In the articles the distance between the transmitter and receiver and number of molecules has been sent is constant. In the end, assuming that the distance between the transmitter and receiver is not fixed and can change, we are proposed a method to determine the best threshold at the receiver that probability of error stay the minimaize.