Changes in how disability is understood have determined an increase in the number of people with disabilities who study at university. Several studies have aimed to investigate the experiences of students with disabilities. However, one difficulty in these studies is that very different types of disability (e.g., reading disabilities as compared to motor disability) are grouped together under the broad label of “students with disability”. Recently, the increase in access to computers and technology has made it possible to distribute questionnaires through the Internet and reach a higher number of participants; however, the use of online questionnaires for conducting research on the experiences of students with disabilities poses theoretical, methodological and ethical challenges to the researcher. Some of these issues are common to questionnaires conducted both online and offline; others, however, are typical of online studies. Here we will review these problems and their consequences in terms of research validity, along with some possible solutions that may minimize the risks of harming the privacy of participants, losing responses, and biasing data.