Due to the increasing importance of the analysis of works of art, many chemical methods have been used in the identification of inorganic compounds, but few of them were aimed at the identification of natural organic compounds. Although mass spectrometry, which is a very sensitive technique, has been used to identify and determine the structure of many types of organic compounds, it has not yet found much application in this area. The present work applies various mass spectrometric techniques to the identification of a number of dyes in pre-Columbian Andean textiles. In its simplest mode a few threads (0.8 mg. of fiber) were inserted into the ion source of the low resolution mass spectrometer via the direct probe and the blue dye was identified as indigotin. Until now the source for the blue dye in Peru was thought to be only Indigofera sufruticos Mill. but this investigation also identified indigotin in a fiber which is known to have been dyed with Indigofera tephrosioides and Vitex sp. verbenaceae. This simple method is not applicable to all dyed fibers. For example, some red and brown dyes could not be identified in this mode. Therefore a second technique was developed, involving the hydrolysis of the red dye to free the dyestuffs from the glycoside and from the fiber. Alizarin and purpurin were identified from a sample dyed with madder root; and purpurin and alizarin were also identified in red fibers from the Paracas culture. Finally, a third variation involves the use of high resolution mass spectrometer which permits one to determine the elemental composition of the compound and to resolve ions derived from components of a mixture that differ in elemental compositions. For example, when a textile sample from Paracas Cavernas that had been painted with a dye from shellfish, was inserted into the ion source of the high resolution mass spectrometer, the dye was identified as 6,6’-dibromoindigotin on the basis of the unique elemental composition of this substance. Similarly, a brown sample dyed with walnut, produced upon hydrolysis gallic acid, caffeinic acid, sakuranetin and quercetin. Juglone, kaempferol and myrecetin were identified by high resolution mass spectrometry. None of them were identified in the brown samples from archaeological sites. There is not a good record of the source of yellow dyes used by the ancient Peruvians. In an attempt to identify these, wool fibers were dyed with some flavonoids since they are common yellow dyes in some plants. Good identification, including differentiation of isomers, was possible from the mass spectra of the flavonoids sakuranetin, fisetin, kaempferol, morin and quercetin. None of the yellow samples from archaeological sites in Peru appeared to contain flavonoid compounds. The present work demonstrates that mass spectrometry has many potential uses in the science of art conservation. The high sensitivity and the possibility to distinguish between natural and synthetic sources make it a valuable tool in this field.