Pigments and inks in five Islamic illuminated manuscripts, dated from 16th to 18th century, were investigated by micro-Raman spectroscopy and SEM-EDX analyses. Micro-Raman spectroscopy was employed for characterization of the pigments and inks used in the manuscripts while SEM-EDX was applied for determination of elemental composition of the metallic and/or organic pigments. Micro-Raman spectroscopy allowed rapid and unambiguous in situ identification of the majority of pigments applied by the calligraphers/scribes without damaging the valuable manuscripts. Most of the pigments were mineral based (vermilion, red lead, lazurite, realgar/pararealgar, orpiment, malachite and its degradation products, atacamite and brochantite). Some organic pigments, like indigo, green organic-Cu complexes (verdigris based) and organic red pigments were also detected. The synthetic blue pigment, Prussian blue was found in the 18th century manuscripts only. Carbon based black was always applied as black ink, while vermilion, a mixture of vermilion and red lead, and, in some cases, organic red, were used as red ink. Metallic pigments (pure gold, a mixture of gold with silver and pure copper) in the illuminations of the manuscript and on the book covers were determined by SEM-EDX technique. (C) 2014 Elsevier B.V. All rights reserved.