The result of these benefits from collaboration is that research can, in principle, be carried out more effectively. Collaboration, however, also entails certain challenges (McGrath, 2004; Government-University-Industry Research Roundtable, 1999). These can take a variety of forms:
Collaborative research may result in additional monetary costs, although it may result in savings for research funding agencies. For inter-institutional, inter-regional and international collaborations, greater travel and material costs are incurred as researchers move from one location to another. For example, equipment and materials may have to be transported, and delicate instrumentation may need to be painstakingly set up again.

Collaboration often demands additional time. For some researchers, time may be more valuable than money. Additional time is often required to prepare a collaborative proposal or to secure joint funds. Different parts of the research may be carried out at different locations, again introducing time adjustments. Time must be spent keeping the collaborators fully informed of progress as well as deciding who is to do what and when to do it. Resolving differences in opinion requires time and respectful listening. Writing up results together may also take more time, especially if there are disagreements over the findings.

Collaboration may result in additional administrative procedures. With more personnel and perhaps several institutions involved, greater effort is usually required to manage the research.

Additional challenges may derive from the university culture. Challenges may arise owing to disagreements over reward systems and promotion criteria, or even because of divergent views over what research is most timely or important to pursue, what methods to employ to carry it out, or what the commercial or ethical implications may be.