Computer-based assessment (CBA) has many advantages for staff and students in higher education. Although we have successfully used diagnostic and formative CBA for a number of years, the introduction of summative assessments raised additional concerns about development time, academic rigour, security and organisation. To explore these issues, a pilot study was set up to assess the running of online (summative) CBA for 240 students taking a first year course in Cell Biology and Biochemistry. We have compared the scores obtained from computer-based marking, with those obtained from: (a) optical mark readers; and (b) traditional hand-marking of scripts. Computer-based marking of text matching questions was initially compromised by spelling errors but these were reduced to an acceptable (, 1%) level by introducing an online subject-specific list of correctly-spelled options. The development and evaluation of secure online examination procedures is also discussed. We conclude that, with these improvements, online CBA can be used successfully for a range of summative assessments in undergraduate Pharmacy courses.