We consider the problem of determining the shape and location of an unknown penetrable object in a perfectly conducting electromagnetic waveguide. The inverse problem is posed in the frequency domain and uses multistatic data in the near field. In particular, we assume that we are given measurements of the electric scattered field due to point sources on a cross-section of the waveguide and measured on the same cross-section, which is away from the scatterer but not in the far field.The problem is solved by using the Linear Sampling Method (LSM) and we also discuss the generalized LSM. We start by giving a brief discussion of the direct problem and its associated interior transmission problem. Then, we adapt and analyze the LSM to deal with the inverse problem. This extends the work on the LSM for perfectly conducting scatterers in a waveguide by one of us (Yang) to the detection of penetrable objects. We provide several useful results concerning reciprocity and the density of fields due to single layer potentials. We also prove the standard results for the LSM in the waveguide context. Finally we give numerical results to show the performance of the method for simple shapes.