In this research, we characterized magnetic and electromagnetic interferences of a two-stage pulse tube cryocooler to a LTc SQUID attached directly to the cold stage of the cryocooler and found the noise sources and proposed methods to reduce their interference on the operation of the LTc SQUID. In chapter one an introduction to cryocoolers and cryocooler based SQUID systems is given. Chapter two presents our method to measure the conducted high frequency electromagnetic interference into the cryocooler cold head via noise paths. In chapter three characterization of low frequency magnetic noises of a two-stage pulse tube cryocooler is presented. Because of the similarity of the profile of the magnetic noise during cool down process with that of the temperature variation we attributed a main noise source to the presence of magnetic regenerative materials located in the second stage. Finally a superconducting lead shield covering over the section containing magnetic regenerative materials at the second stage is proposed to reduce the interference of the noise to the SQUID attached directly on the second stage cold head.