Phonon thermal conductivities in both growth and in-plane directions of Si/Ge superlattices (SLs) with perfect and rough interfaces are calculated by using a lattice dynamics model. In addition to the general trend, the results show that there exist fluctuations of thermal conductivity in both directions for SLs with even or odd number of layers when the layer thickness is small. Thermal conductivities in both directions of Si/Ge SLs with rough interfaces are shown to be much lower than those of SLs with perfect interfaces. To understand the influences of rough interfaces, thermal conductivities of homogeneous alloy are further calculated and compared. The results show that along the in-plane direction, the thermal conductivity of SLs with rough interfaces is about the same as that of random alloy, while in the growth direction it is lower than that of the random alloy.