Molecular investigation of an outbreak of HIV at Glenochil Prison contributed to the conviction of a former Glenochil drug injector, Mr Stephen Kelly, for culpably and recklessly transmitting HIV to a female sexual partner. We explain why the case of Rv Kelly has brought the medical and legal professions into conflict and explore its implications for public health and molecular science in Scotland. Firstly, even a modest decline in the uptake of HIV testing by those who are actually infected could herald a one third increase in new sexually transmitted HIV infections. Secondly, there is now need for a national proforma to assure the quality and legality of HIV counselling in Scotland as a safeguard for both counsellors and clients. Thirdly, we discuss curtailment of molecular research investigations with the potential to discover incriminating evidence about HIV transmissions unless laboratory protocols, or legal safeguards, can be designed which obviate deductive disclosure about individuals. Urgent review by the Scottish Executive is required to minimise negative impacts of the Glenochil judgement on public health and molecular science.