A study of defects that are observed in Si MBE layers under certain growth conditions is reported. Optical microscopy examinations of unetched and etched layers reveal particle-like defects of micron size, stacking faults, dislocations, and saucer pits. TEM shows interfacial defects of tens of Angstroms size at the substrate-epitaxial layer interface. Reproducible defect densities are given for various in-situ cleaning procedures.