Assessment of the relative impact of diseases and pathogens is important for agencies and other organizations charged with providing disease surveillance, management and control. It also helps funders of disease-related research to identify the most important areas for investment. Decisions as to which pathogens or diseases to target are often made using complex risk assessment approaches; however, these usually involve evaluating a large number of hazards as it is rarely feasible to conduct an in-depth appraisal of each. Here we propose the use of the H-index (or Hirsch index) as an alternative rapid, repeatable and objective means of assessing pathogen impact. H-index scores for 1,414 human pathogens were obtained from the Institute for Scientific Information's Web of Science (WOS) in July/August 2010. Scores were compared for zoonotic/non-zoonotic, and emerging/non-emerging pathogens, and across taxonomic groups. H-indices for a subset of pathogens were compared with Disability Adjusted Life Year (DALY) estimates for the diseases they cause. H-indices ranged from 0 to 456, with a median of 11. Emerging pathogens had higher H-indices than non-emerging pathogens. Zoonotic pathogens tended to have higher H-indices than human-only pathogens, although the opposite was observed for viruses. There was a significant correlation between the DALY of a disease and the H-index of the pathogen(s) that cause it. Therefore, scientific interest, as measured by the H-index, appears to be a reflection of the true impact of pathogens. The H-index method can be utilized to set up an objective, repeatable and readily automated system for assessing pathogen or disease impact.