MODOMICS is a comprehensive database for RNA modification pathways, integrating information on modified nucleosides, their localization, biosynthesis pathways, and enzymes involved. It provides literature data and links to other databases, including protein sequence and structure data. The database includes a wide range of RNA modifications and pathways, though enzyme data are limited to *E. coli* and *S. cerevisiae*, with sequence alignments only for tRNAs from these organisms. Future updates will include data from other organisms. MODOMICS allows querying by nucleoside type, RNA type, nucleoside position, reaction type, and enzyme name or sequence. Data presentation options include pathway graphs, multiple sequence alignments, and tabular forms with enzyme and literature data. The database is accessible via the web at http://genesilico.pl/modomics/. MODOMICS is a relational database linking modification pathways, RNA-modifying enzymes, and target RNA sequences. Pathways are visualized as graphs using GRAPHVIZ, with nodes representing modified nucleosides and edges representing transformations. The database includes five graphs for known modifications of adenosine, cytidine, guanosine, uridine, and the queuosine pathway. The 'PATHWAYS' menu allows filtering by organism, organellum, RNA type, and hypermodifications. The 'ENZYMES' menu lists enzymes from *E. coli* and *S. cerevisiae*, with information on gene names, amino acid sequences, structures, and literature references. The 'RNAs' menu provides multiple sequence alignments of tRNA sequences from *S. cerevisiae* and *E. coli*. MODOMICS is freely accessible for research and can be used to predict RNA modifications from DNA sequences. The database is supported by publicly available data and is available at the specified URL. The authors acknowledge Daylight Chemical Information Systems Inc. for providing the SMI2GIF service and thank the funding bodies for their support. The database is a valuable resource for researchers studying RNA modifications and their biological functions.MODOMICS is a comprehensive database for RNA modification pathways, integrating information on modified nucleosides, their localization, biosynthesis pathways, and enzymes involved. It provides literature data and links to other databases, including protein sequence and structure data. The database includes a wide range of RNA modifications and pathways, though enzyme data are limited to *E. coli* and *S. cerevisiae*, with sequence alignments only for tRNAs from these organisms. Future updates will include data from other organisms. MODOMICS allows querying by nucleoside type, RNA type, nucleoside position, reaction type, and enzyme name or sequence. Data presentation options include pathway graphs, multiple sequence alignments, and tabular forms with enzyme and literature data. The database is accessible via the web at http://genesilico.pl/modomics/. MODOMICS is a relational database linking modification pathways, RNA-modifying enzymes, and target RNA sequences. Pathways are visualized as graphs using GRAPHVIZ, with nodes representing modified nucleosides and edges representing transformations. The database includes five graphs for known modifications of adenosine, cytidine, guanosine, uridine, and the queuosine pathway. The 'PATHWAYS' menu allows filtering by organism, organellum, RNA type, and hypermodifications. The 'ENZYMES' menu lists enzymes from *E. coli* and *S. cerevisiae*, with information on gene names, amino acid sequences, structures, and literature references. The 'RNAs' menu provides multiple sequence alignments of tRNA sequences from *S. cerevisiae* and *E. coli*. MODOMICS is freely accessible for research and can be used to predict RNA modifications from DNA sequences. The database is supported by publicly available data and is available at the specified URL. The authors acknowledge Daylight Chemical Information Systems Inc. for providing the SMI2GIF service and thank the funding bodies for their support. The database is a valuable resource for researchers studying RNA modifications and their biological functions.