According to improper factors in museums, storages and libraries environments, surface deposits and different types of dirt can contaminate the surface of parchment manuscripts. The brittleness, hardness, corrosion, discoloration and stains from different sources are considered to be some of the deterioration forms resulting from the reaction between parchment and stains. This study aims to make a survey on different stains found on parchment, explain the forms and mechanisms of their deterioration, and explain the traditional and laser cleaning techniques used for stains removal. Moisture, dusts, soot, blood, iron rust, adhesives residues and microorganisms stains are considered the most common stains on parchment manuscripts. This study confirms that mechanical cleaning, chemical techniques, cleaning with organic solvents, and laser cleaning have been used. Sometimes cleaning processes especially traditional cleaning can lead to pressure, irreversible damage, surface or molecular structural damage and denaturation of collagen. This latter can occur in advanced states of degradation. Laser cleaning is preferred for parchment because it is a contactless, chemical free and non-destructive procedure. Analysis and investigation should be used for the evaluation of deterioration and conservation treatments. The study reveals that all cleaning techniques of parchment manuscripts have advantages and disadvantages and all are required, but the state of preservation and nature of stains will direct the selection of the suitable cleaning technique. Sometimes one or more techniques can be used for the removal of the same stains on the same manuscript.