New chemotherapies are urgently needed for the parasitic infections of animals and for the tropical diseases of man. Rational molecular design approaches to attempt to discover such products require a massive investment of resources up-front of actual chemical synthesis. However, such investment is justified, since chemical synthesis itself is highly resource-consuming. The fact that few targets have yet been validated to justify a rational approach is an argument only to get on and validate more. Not all the components of molecular design can yet be done totally rationally, but this is not an argument against applying this approach where it is possible. Absence of a successful track record is inevitable for any newly emerging technology. It is too early to draw conclusions about the relative costs of rational design versus empirical synthesis, since the former is only now beginning to become reality and the latter is in the middle of a (combinatorial) revolution. Similarly, it is too soon to predict with certainty which of these two approaches will prevail in the long run. However, they lend themselves to parallel tracks, so both may well continue for the foreseeable future. Current concerns about who would develop successful discoveries are not reasons for stopping discovery research. Indeed, a string of putative products held at the discovery/development interface would be useful ammunition to those trying to develop partnerships such as a Tropical Diseases R&D Alliance aimed at carrying out such work and sharing costs.