This work reports on the first systematic study using secondary ion mass spectrometry with MeV ions (MeV-SIMS) for analysis of synthetic organic pigments (SOPs) that can be usually found in modern and contemporary art paints. In order to prove the applicability of the method to different chemical classes of SOPs, 17 pigments were selected for the analyses. The focus was on blue and green phthalocyanines, yellow and red (naphthol AS) azo pigments, red quinacridone, anthraquinone, and diketopyrrolo-pyrrole pigments. Since there are no reference spectra available for this technique, pure pigment powders were measured first to create a database. Simple two-component paint systems were also prepared for testing purposes by mixing synthetic organic pigments with alkyd and acrylic binders. Commercial paints that contain the SOPs with identical C.I. numbers as in the prepared two-component samples were analyzed. All pigments were successfully identified in commercial products in the MeV-SIMS mass spectra through molecular and larger specific fragment ion peaks in the positive-ion mode. The main advantages of MeV-SIMS over other techniques used in SOPs identification, like pyrolysis gas chromatography mass spectrometry (Py-GC/MS), direct-temperature resolved mass spectrometry (DTMS), and laser desorption ionization mass spectrometry (LDIMS), can be summarized as follows: (i) pigments and binders can be detected simultaneously in the same mass spectrum acquired over a short measurement time (up to 500 s), (ii) only small sample flakes are required for the measurements, which are analyzed without any chemical treatment prior to the analyses, (iii) samples are not consumed during the analyses and can be reused for other measurements, e.g., multielemental analysis by other ion beam analysis (IBA) techniques, such as particle-induced X-ray emission (PIXE). Compared to, e.g., Raman spectroscopy, the significant benefit of MeV-SIMS is the exact identification of the SOPs in the paints even if pigments of similar structures are measured.