Purpose: The purpose of this paper is to relate the problems identified about scholarly journal publishing in Malaysia to establish motivation for the system development; to describe the design of MyCite, a Malaysian citation indexing system and to highlight the added value to journals and articles indexed through the generation of bibliometrics performance reports. Design/methodology/approach: The system uses a rapid prototyping method, modeling the functions identified in the Web of Science databases and Scopus, as the Ministry of Higher Education Malaysia requires the system to be ready within a year, mainly to help improve the quality, accessibility and performance of Malaysian scholarly journals. Findings: The paper shows the relational tables and module functions in MyCite; highlights the value added to bibliographic data through performance reports of authors, journals, institutions, country and bibliographical control of Malaysian journals; and provides performance tables of top authors, rank list of 75 journals by yearly impact factor, and other bibliometric indices. Research limitations/implications: The paper highlight the problems in gaining access to full contents of journals, authors' adoption of variant names, and the vast variations in referencing style adopted by publishers, which may result in inaccurate counting and lost citations. Originality/value: The strength of MyCite is in its reference editor module, which is a programme that segments article references into manageable chunks that helps speed up the data preparation for citation counting. MyCite improves the availability and visibility of Malaysian journals, enriches national research content, and provides better knowledge of national research outputs funded by universities and research institutions. (Contains 10 tables and 6 figures.)