Abstract Background It has been well established that research is not addressing health needs in a balanced way — much more research is conducted on diseases with more burden in high-income countries than on those with more burden in lower-income countries. In this study, we explore whether these imbalances persist and inquire about the possible influence of three factors, namely geography, industry and publication incentives. Methods We use WHO data on the Global Burden of Disease as a proxy measure of health needs and bibliometric information as a proxy for research efforts. Scientific publications on diseases were collected from MEDLINE using MeSH terms to identify relevant publications. We used Web of Science to collect author affiliations and citation data. We developed a correspondence table between WHO ICD-10 and MeSH descriptors to compare global health needs and research efforts. This correspondence table is available as supplementary material. Results Research output is heavily concentrated in high-income countries and is mainly focused on their health needs, resulting in a relative lack of attention to diseases in lower income countries. A new finding is that diseases with a similar burden in high- and middle-income countries are also under-researched, both globally and in relation to disease burden in high- and middle-income countries. Global industrial R&D is found to be very similar to the focus of public research. Diseases more prevalent in high-income countries generate ten-fold more research attention than those in low-income countries. We find no discernible preference towards diseases of high-income countries versus those of low-income countries in the top 25% most prestigious journals. However, in middle-income countries, citation rates are substantially lower for diseases most prevalent in low- and middle-income countries. Conclusions From a global perspective, the imbalance between research needs and research efforts persists as most of the research effort concentrates on diseases affecting high-income countries. Both pharmaceutical companies and the public sector also tend to focus on diseases with more burden in high-income countries. Our findings indicate that researchers in middle-income countries receive more citations when researching diseases more prevalent in high-income countries, and this may divert the attention of researchers in these countries from diseases more prevalent in their contexts.